Job ID = 6365928 SRX = SRX043861 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:36 prefetch.2.10.7: 1) Downloading 'SRR107320'... 2020-06-15T22:32:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:18 prefetch.2.10.7: 'SRR107320' is valid 2020-06-15T22:33:18 prefetch.2.10.7: 1) 'SRR107320' was downloaded successfully Read 6335499 spots for SRR107320/SRR107320.sra Written 6335499 spots for SRR107320/SRR107320.sra 2020-06-15T22:33:47 prefetch.2.10.7: 1) Downloading 'SRR107321'... 2020-06-15T22:33:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:26 prefetch.2.10.7: 'SRR107321' is valid 2020-06-15T22:34:26 prefetch.2.10.7: 1) 'SRR107321' was downloaded successfully Read 4412948 spots for SRR107321/SRR107321.sra Written 4412948 spots for SRR107321/SRR107321.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: 00:00:51 10748447 reads; of these: 10748447 (100.00%) were unpaired; of these: 10077394 (93.76%) aligned 0 times 586367 (5.46%) aligned exactly 1 time 84686 (0.79%) aligned >1 times 6.24% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 18596 / 671053 = 0.0277 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 @ Tue, 16 Jun 2020 07:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.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 @ Tue, 16 Jun 2020 07:36:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:22: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:22: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:22: #1 total tags in treatment: 652457 INFO @ Tue, 16 Jun 2020 07:36:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:36:22: #1 tags after filtering in treatment: 652457 INFO @ Tue, 16 Jun 2020 07:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:22: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 07:36:22: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:22: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:36:22: #2 alternative fragment length(s) may be 44,124,549 bps INFO @ Tue, 16 Jun 2020 07:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.05_model.r WARNING @ Tue, 16 Jun 2020 07:36:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:36:23: #2 You may need to consider one of the other alternative d(s): 44,124,549 WARNING @ Tue, 16 Jun 2020 07:36:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:36:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.05_summits.bed INFO @ Tue, 16 Jun 2020 07:36:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Tue, 16 Jun 2020 07:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.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 @ Tue, 16 Jun 2020 07:36:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:52: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:52: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:52: #1 total tags in treatment: 652457 INFO @ Tue, 16 Jun 2020 07:36:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:36:52: #1 tags after filtering in treatment: 652457 INFO @ Tue, 16 Jun 2020 07:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:53: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 07:36:53: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:53: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:36:53: #2 alternative fragment length(s) may be 44,124,549 bps INFO @ Tue, 16 Jun 2020 07:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.10_model.r WARNING @ Tue, 16 Jun 2020 07:36:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:36:53: #2 You may need to consider one of the other alternative d(s): 44,124,549 WARNING @ Tue, 16 Jun 2020 07:36:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:36:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.10_summits.bed INFO @ Tue, 16 Jun 2020 07:36:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 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 @ Tue, 16 Jun 2020 07:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.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 @ Tue, 16 Jun 2020 07:37:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:37:19: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:37:23: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:37:23: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:37:23: #1 total tags in treatment: 652457 INFO @ Tue, 16 Jun 2020 07:37:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:37:23: #1 tags after filtering in treatment: 652457 INFO @ Tue, 16 Jun 2020 07:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:23: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 07:37:23: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:23: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:37:23: #2 alternative fragment length(s) may be 44,124,549 bps INFO @ Tue, 16 Jun 2020 07:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.20_model.r WARNING @ Tue, 16 Jun 2020 07:37:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:37:23: #2 You may need to consider one of the other alternative d(s): 44,124,549 WARNING @ Tue, 16 Jun 2020 07:37:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:37:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043861/SRX043861.20_summits.bed INFO @ Tue, 16 Jun 2020 07:37:25: Done! pass1 - making usageList (3 chroms): 3 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling