Job ID = 6497555 SRX = SRX657410 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:46:59 prefetch.2.10.7: 1) Downloading 'SRR1520419'... 2020-06-25T21:47:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:48:24 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:48:24 prefetch.2.10.7: 'SRR1520419' is valid 2020-06-25T21:48:24 prefetch.2.10.7: 1) 'SRR1520419' was downloaded successfully Read 8712390 spots for SRR1520419/SRR1520419.sra Written 8712390 spots for SRR1520419/SRR1520419.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:37 8712390 reads; of these: 8712390 (100.00%) were unpaired; of these: 2437496 (27.98%) aligned 0 times 5096766 (58.50%) aligned exactly 1 time 1178128 (13.52%) aligned >1 times 72.02% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 543545 / 6274894 = 0.0866 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, 26 Jun 2020 06:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.bam'] # control file = None # effective genome size = 9.00e+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, 26 Jun 2020 06:53:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:53:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:53:59: 1000000 INFO @ Fri, 26 Jun 2020 06:54:04: 2000000 INFO @ Fri, 26 Jun 2020 06:54:10: 3000000 INFO @ Fri, 26 Jun 2020 06:54:15: 4000000 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, 26 Jun 2020 06:54:21: 5000000 INFO @ Fri, 26 Jun 2020 06:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.bam'] # control file = None # effective genome size = 9.00e+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, 26 Jun 2020 06:54:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:54:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:54:25: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 06:54:25: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 06:54:25: #1 total tags in treatment: 5731349 INFO @ Fri, 26 Jun 2020 06:54:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:54:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:54:25: #1 tags after filtering in treatment: 5731349 INFO @ Fri, 26 Jun 2020 06:54:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:54:25: #1 finished! INFO @ Fri, 26 Jun 2020 06:54:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:54:26: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 06:54:26: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 06:54:26: start model_add_line... INFO @ Fri, 26 Jun 2020 06:54:26: start X-correlation... INFO @ Fri, 26 Jun 2020 06:54:26: end of X-cor INFO @ Fri, 26 Jun 2020 06:54:26: #2 finished! INFO @ Fri, 26 Jun 2020 06:54:26: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 06:54:26: #2 alternative fragment length(s) may be 4,47,542,565 bps INFO @ Fri, 26 Jun 2020 06:54:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.05_model.r WARNING @ Fri, 26 Jun 2020 06:54:26: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:54:26: #2 You may need to consider one of the other alternative d(s): 4,47,542,565 WARNING @ Fri, 26 Jun 2020 06:54:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:54:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:54:29: 1000000 INFO @ Fri, 26 Jun 2020 06:54:34: 2000000 INFO @ Fri, 26 Jun 2020 06:54:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:54:40: 3000000 INFO @ Fri, 26 Jun 2020 06:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.05_summits.bed INFO @ Fri, 26 Jun 2020 06:54:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:54:46: 4000000 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, 26 Jun 2020 06:54:51: 5000000 INFO @ Fri, 26 Jun 2020 06:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.bam'] # control file = None # effective genome size = 9.00e+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, 26 Jun 2020 06:54:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:54:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:54:56: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 06:54:56: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 06:54:56: #1 total tags in treatment: 5731349 INFO @ Fri, 26 Jun 2020 06:54:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:54:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:54:56: #1 tags after filtering in treatment: 5731349 INFO @ Fri, 26 Jun 2020 06:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:54:56: #1 finished! INFO @ Fri, 26 Jun 2020 06:54:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:54:56: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 06:54:56: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 06:54:56: start model_add_line... INFO @ Fri, 26 Jun 2020 06:54:56: start X-correlation... INFO @ Fri, 26 Jun 2020 06:54:56: end of X-cor INFO @ Fri, 26 Jun 2020 06:54:56: #2 finished! INFO @ Fri, 26 Jun 2020 06:54:56: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 06:54:56: #2 alternative fragment length(s) may be 4,47,542,565 bps INFO @ Fri, 26 Jun 2020 06:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.10_model.r WARNING @ Fri, 26 Jun 2020 06:54:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:54:56: #2 You may need to consider one of the other alternative d(s): 4,47,542,565 WARNING @ Fri, 26 Jun 2020 06:54:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:54:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:54:59: 1000000 INFO @ Fri, 26 Jun 2020 06:55:04: 2000000 INFO @ Fri, 26 Jun 2020 06:55:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:55:10: 3000000 INFO @ Fri, 26 Jun 2020 06:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.10_summits.bed INFO @ Fri, 26 Jun 2020 06:55:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:55:16: 4000000 INFO @ Fri, 26 Jun 2020 06:55:22: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:55:27: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 06:55:27: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 06:55:27: #1 total tags in treatment: 5731349 INFO @ Fri, 26 Jun 2020 06:55:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:55:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:55:27: #1 tags after filtering in treatment: 5731349 INFO @ Fri, 26 Jun 2020 06:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:55:27: #1 finished! INFO @ Fri, 26 Jun 2020 06:55:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:55:27: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 06:55:27: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 06:55:27: start model_add_line... INFO @ Fri, 26 Jun 2020 06:55:27: start X-correlation... INFO @ Fri, 26 Jun 2020 06:55:27: end of X-cor INFO @ Fri, 26 Jun 2020 06:55:27: #2 finished! INFO @ Fri, 26 Jun 2020 06:55:27: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 06:55:27: #2 alternative fragment length(s) may be 4,47,542,565 bps INFO @ Fri, 26 Jun 2020 06:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.20_model.r WARNING @ Fri, 26 Jun 2020 06:55:34: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:55:34: #2 You may need to consider one of the other alternative d(s): 4,47,542,565 WARNING @ Fri, 26 Jun 2020 06:55:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 06:55:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:55:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX657410/SRX657410.20_summits.bed INFO @ Fri, 26 Jun 2020 06:55:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 1 millis CompletedMACS2peakCalling