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‎salmon/quants_NGS130/aux_info/ambig_info.tsv

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‎salmon/quants_NGS130/aux_info/expected_bias.gz

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‎salmon/quants_NGS130/aux_info/fld.gz

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‎salmon/quants_NGS130/aux_info/meta_info.json

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{
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"salmon_version": "1.3.0",
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"samp_type": "none",
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"opt_type": "vb",
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"quant_errors": [],
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"num_libraries": 1,
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"library_types": [
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"IU"
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],
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"frag_dist_length": 1001,
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"frag_length_mean": 310.17621264012208,
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"frag_length_sd": 124.24614429810318,
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"seq_bias_correct": false,
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"gc_bias_correct": false,
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"num_bias_bins": 4096,
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"mapping_type": "mapping",
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"keep_duplicates": false,
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"num_valid_targets": 27017,
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"num_decoy_targets": 0,
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"num_eq_classes": 1992,
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"serialized_eq_classes": false,
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"eq_class_properties": [
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"range_factorized",
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"gzipped"
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],
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"length_classes": [
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714,
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1041,
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1506,
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2340,
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26400
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],
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"index_seq_hash": "1e77465722ebc06bb1c42bcb8dd29be193f4adc8095fdfa904b079e94fd47c4e",
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"index_name_hash": "498d14c705101fe2e2fb0a1d14098c9b296c99d10a1ea80685303fd2c1d53ae9",
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"index_seq_hash512": "23c80831975e7dc5ed362c2b1af4ec81efee6747f817d8580d45f34ba2eb7377bb4ff92415c57cf2f1184ef11abe9bccaf6e6c9cea2709e4cdf0092b3ad87af2",
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"index_name_hash512": "d529c0d592bc286bacb414dca64f45dee737185814c293fa6a765e9963079e32a46fc43baa0884c2b3538bc4bdc8d644b6a687b11fb3842fe6eb1b2f20f79994",
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"index_decoy_seq_hash": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
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"index_decoy_name_hash": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
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"num_bootstraps": 0,
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"num_processed": 43559176,
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"num_mapped": 6121447,
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"num_decoy_fragments": 0,
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"num_dovetail_fragments": 2676733,
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"num_fragments_filtered_vm": 28537710,
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"num_alignments_below_threshold_for_mapped_fragments_vm": 43911649,
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"percent_mapped": 14.05317446776312,
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"call": "quant",
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"start_time": "Tue Sep 22 22:18:14 2020",
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"end_time": "Tue Sep 22 22:22:11 2020"
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}

‎salmon/quants_NGS130/aux_info/observed_bias.gz

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‎salmon/quants_NGS130/aux_info/observed_bias_3p.gz

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‎salmon/quants_NGS130/cmd_info.json

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{
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"salmon_version": "1.3.0",
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"index": "CCDS_nucleotide.current",
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"libType": "A",
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"mates1": "/nethome/xcai/WeiLi_RNAdata/NGS130_S23_L001_R1_001.fastq",
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"mates2": "/nethome/xcai/WeiLi_RNAdata/NGS130_S23_L001_R2_001.fastq",
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"threads": "10",
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"validateMappings": [],
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"output": "quants_NGS130/",
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"auxDir": "aux_info"
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}

‎salmon/quants_NGS130/libParams/flenDist.txt

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‎salmon/quants_NGS130/lib_format_counts.json

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{
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"read_files": "[ /nethome/xcai/WeiLi_RNAdata/NGS130_S23_L001_R1_001.fastq, /nethome/xcai/WeiLi_RNAdata/NGS130_S23_L001_R2_001.fastq]",
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"expected_format": "IU",
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"compatible_fragment_ratio": 1.0,
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"num_compatible_fragments": 6121447,
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"num_assigned_fragments": 6121447,
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"num_frags_with_concordant_consistent_mappings": 3799706,
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"num_frags_with_inconsistent_or_orphan_mappings": 2322678,
9+
"strand_mapping_bias": 0.512755197375797,
10+
"MSF": 0,
11+
"OSF": 0,
12+
"ISF": 1948319,
13+
"MSR": 0,
14+
"OSR": 0,
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"ISR": 1851387,
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"SF": 1703641,
17+
"SR": 619037,
18+
"MU": 0,
19+
"OU": 0,
20+
"IU": 0,
21+
"U": 0
22+
}

‎salmon/quants_NGS130/logs/salmon_quant.log

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[2020-09-22 22:18:14.424] [jointLog] [info] setting maxHashResizeThreads to 10
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[2020-09-22 22:18:14.424] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
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[2020-09-22 22:18:14.424] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
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[2020-09-22 22:18:14.424] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
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[2020-09-22 22:18:14.424] [jointLog] [info] parsing read library format
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[2020-09-22 22:18:14.424] [jointLog] [info] There is 1 library.
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[2020-09-22 22:18:14.469] [jointLog] [info] Loading pufferfish index
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[2020-09-22 22:18:14.471] [jointLog] [info] Loading dense pufferfish index.
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[2020-09-22 22:18:14.675] [jointLog] [info] done
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[2020-09-22 22:18:14.675] [jointLog] [info] Index contained 27,017 targets
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[2020-09-22 22:18:14.701] [jointLog] [info] Number of decoys : 0
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[2020-09-22 22:18:17.192] [jointLog] [info] Automatically detected most likely library type as IU
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[2020-09-22 22:22:10.049] [jointLog] [info] Computed 1,992 rich equivalence classes for further processing
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[2020-09-22 22:22:10.049] [jointLog] [info] Counted 6,121,447 total reads in the equivalence classes
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[2020-09-22 22:22:10.053] [jointLog] [info] Number of mappings discarded because of alignment score : 43,911,649
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[2020-09-22 22:22:10.053] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 28,537,710
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[2020-09-22 22:22:10.053] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
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[2020-09-22 22:22:10.053] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,676,733
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[2020-09-22 22:22:10.053] [jointLog] [info] Mapping rate = 14.0532%
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[2020-09-22 22:22:10.053] [jointLog] [info] finished quantifyLibrary()
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[2020-09-22 22:22:10.057] [jointLog] [info] Starting optimizer
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[2020-09-22 22:22:10.112] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
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[2020-09-22 22:22:10.115] [jointLog] [info] iteration = 0 | max rel diff. = 2490.65
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[2020-09-22 22:22:10.050] [fileLog] [info]
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At end of round 0
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==================
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Observed 43559176 total fragments (43559176 in most recent round)
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[2020-09-22 22:22:10.260] [jointLog] [info] iteration = 100 | max rel diff. = 0.850271
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[2020-09-22 22:22:10.403] [jointLog] [info] iteration = 200 | max rel diff. = 0.145546
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[2020-09-22 22:22:10.545] [jointLog] [info] iteration = 300 | max rel diff. = 0.0996828
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[2020-09-22 22:22:10.688] [jointLog] [info] iteration = 400 | max rel diff. = 0.0821896
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[2020-09-22 22:22:10.831] [jointLog] [info] iteration = 500 | max rel diff. = 0.0141035
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[2020-09-22 22:22:10.974] [jointLog] [info] iteration = 600 | max rel diff. = 0.175783
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[2020-09-22 22:22:11.117] [jointLog] [info] iteration = 700 | max rel diff. = 0.0248447
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[2020-09-22 22:22:11.183] [jointLog] [info] iteration = 747 | max rel diff. = 0.00484977
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[2020-09-22 22:22:11.184] [jointLog] [info] Finished optimizer
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[2020-09-22 22:22:11.184] [jointLog] [info] writing output
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[2020-09-22 22:22:11.228] [jointLog] [warning] NOTE: Read Lib [[ /nethome/xcai/WeiLi_RNAdata/NGS130_S23_L001_R1_001.fastq, /nethome/xcai/WeiLi_RNAdata/NGS130_S23_L001_R2_001.fastq]] :
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Detected a *potential* strand bias > 1% in an unstranded protocol check the file: quants_NGS130/lib_format_counts.json for details
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