Job ID = 10223850 SRX = ERX4439602 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:25:33 prefetch.2.10.7: 1) Downloading 'ERR4501531'... 2020-10-15T23:25:33 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:26:23 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:26:23 prefetch.2.10.7: 'ERR4501531' is valid 2020-10-15T23:26:23 prefetch.2.10.7: 1) 'ERR4501531' was downloaded successfully 2020-10-15T23:26:51 prefetch.2.10.7: 'ERR4501531' has 5 unresolved dependencies 2020-10-15T23:26:51 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:26:51 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:27:03 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:27:03 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:27:03 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:27:03 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:27:16 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:27:16 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:27:16 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:27:16 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:27:28 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:27:28 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:27:28 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:27:28 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:27:39 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:27:39 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:27:39 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:27:39 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:27:49 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:27:49 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 2830100 spots for ERR4501531/ERR4501531.sra Written 2830100 spots for ERR4501531/ERR4501531.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:57 2830100 reads; of these: 2830100 (100.00%) were paired; of these: 1545243 (54.60%) aligned concordantly 0 times 1012223 (35.77%) aligned concordantly exactly 1 time 272634 (9.63%) aligned concordantly >1 times ---- 1545243 pairs aligned concordantly 0 times; of these: 276940 (17.92%) aligned discordantly 1 time ---- 1268303 pairs aligned 0 times concordantly or discordantly; of these: 2536606 mates make up the pairs; of these: 2024702 (79.82%) aligned 0 times 227041 (8.95%) aligned exactly 1 time 284863 (11.23%) aligned >1 times 64.23% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 166459 / 1527466 = 0.1090 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:33:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Oct 2020 08:33:20: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:33:20: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:33:28: 1000000 INFO @ Fri, 16 Oct 2020 08:33:37: 2000000 INFO @ Fri, 16 Oct 2020 08:33:47: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:33:49: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:33:49: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:33:49: #1 total tags in treatment: 1154750 INFO @ Fri, 16 Oct 2020 08:33:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:33:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:33:49: #1 tags after filtering in treatment: 823479 INFO @ Fri, 16 Oct 2020 08:33:49: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 16 Oct 2020 08:33:49: #1 finished! INFO @ Fri, 16 Oct 2020 08:33:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:33:49: #2 number of paired peaks: 340 WARNING @ Fri, 16 Oct 2020 08:33:49: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Fri, 16 Oct 2020 08:33:49: start model_add_line... INFO @ Fri, 16 Oct 2020 08:33:49: start X-correlation... INFO @ Fri, 16 Oct 2020 08:33:49: end of X-cor INFO @ Fri, 16 Oct 2020 08:33:49: #2 finished! INFO @ Fri, 16 Oct 2020 08:33:49: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:33:49: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.05_model.r WARNING @ Fri, 16 Oct 2020 08:33:49: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:33:49: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:33:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:33:49: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:33:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Oct 2020 08:33:50: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:33:50: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:33:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:33:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:33:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:33:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.05_summits.bed INFO @ Fri, 16 Oct 2020 08:33:53: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (615 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:33:57: 1000000 INFO @ Fri, 16 Oct 2020 08:34:04: 2000000 INFO @ Fri, 16 Oct 2020 08:34:12: 3000000 INFO @ Fri, 16 Oct 2020 08:34:14: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:34:14: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:34:14: #1 total tags in treatment: 1154750 INFO @ Fri, 16 Oct 2020 08:34:14: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:34:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:34:14: #1 tags after filtering in treatment: 823479 INFO @ Fri, 16 Oct 2020 08:34:14: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 16 Oct 2020 08:34:14: #1 finished! INFO @ Fri, 16 Oct 2020 08:34:14: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:34:14: #2 number of paired peaks: 340 WARNING @ Fri, 16 Oct 2020 08:34:14: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Fri, 16 Oct 2020 08:34:14: start model_add_line... INFO @ Fri, 16 Oct 2020 08:34:14: start X-correlation... INFO @ Fri, 16 Oct 2020 08:34:14: end of X-cor INFO @ Fri, 16 Oct 2020 08:34:14: #2 finished! INFO @ Fri, 16 Oct 2020 08:34:14: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:34:14: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.10_model.r WARNING @ Fri, 16 Oct 2020 08:34:14: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:34:14: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:34:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:34:14: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:34:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:34:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:34:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:34:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.10_summits.bed INFO @ Fri, 16 Oct 2020 08:34:17: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (502 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:34:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Oct 2020 08:34:20: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:34:20: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:34:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:34:37: 2000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:34:46: 3000000 INFO @ Fri, 16 Oct 2020 08:34:49: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:34:49: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:34:49: #1 total tags in treatment: 1154750 INFO @ Fri, 16 Oct 2020 08:34:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:34:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:34:49: #1 tags after filtering in treatment: 823479 INFO @ Fri, 16 Oct 2020 08:34:49: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 16 Oct 2020 08:34:49: #1 finished! INFO @ Fri, 16 Oct 2020 08:34:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:34:49: #2 number of paired peaks: 340 WARNING @ Fri, 16 Oct 2020 08:34:49: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Fri, 16 Oct 2020 08:34:49: start model_add_line... INFO @ Fri, 16 Oct 2020 08:34:49: start X-correlation... INFO @ Fri, 16 Oct 2020 08:34:49: end of X-cor INFO @ Fri, 16 Oct 2020 08:34:49: #2 finished! INFO @ Fri, 16 Oct 2020 08:34:49: #2 predicted fragment length is 150 bps INFO @ Fri, 16 Oct 2020 08:34:49: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 16 Oct 2020 08:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.20_model.r WARNING @ Fri, 16 Oct 2020 08:34:49: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:34:49: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 16 Oct 2020 08:34:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:34:49: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:34:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439602/ERX4439602.20_summits.bed INFO @ Fri, 16 Oct 2020 08:34:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling