Job ID = 6368010 SRX = SRX466473 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:19:21 prefetch.2.10.7: 1) Downloading 'SRR1163539'... 2020-06-16T00:19:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:21 prefetch.2.10.7: 'SRR1163539' is valid 2020-06-16T00:21:21 prefetch.2.10.7: 1) 'SRR1163539' was downloaded successfully Read 10041623 spots for SRR1163539/SRR1163539.sra Written 10041623 spots for SRR1163539/SRR1163539.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: 00:02:14 10041623 reads; of these: 10041623 (100.00%) were unpaired; of these: 595585 (5.93%) aligned 0 times 8476989 (84.42%) aligned exactly 1 time 969049 (9.65%) aligned >1 times 94.07% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 2219659 / 9446038 = 0.2350 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 09:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.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 09:26:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:49: 1000000 INFO @ Tue, 16 Jun 2020 09:26:55: 2000000 INFO @ Tue, 16 Jun 2020 09:27:02: 3000000 INFO @ Tue, 16 Jun 2020 09:27:08: 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 @ Tue, 16 Jun 2020 09:27:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.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 09:27:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:15: 5000000 INFO @ Tue, 16 Jun 2020 09:27:21: 1000000 INFO @ Tue, 16 Jun 2020 09:27:22: 6000000 INFO @ Tue, 16 Jun 2020 09:27:28: 2000000 INFO @ Tue, 16 Jun 2020 09:27:30: 7000000 INFO @ Tue, 16 Jun 2020 09:27:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:27:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:27:31: #1 total tags in treatment: 7226379 INFO @ Tue, 16 Jun 2020 09:27:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:31: #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 09:27:31: #1 tags after filtering in treatment: 7226379 INFO @ Tue, 16 Jun 2020 09:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:32: #2 number of paired peaks: 591 WARNING @ Tue, 16 Jun 2020 09:27:32: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:32: #2 predicted fragment length is 84 bps INFO @ Tue, 16 Jun 2020 09:27:32: #2 alternative fragment length(s) may be 4,84,90 bps INFO @ Tue, 16 Jun 2020 09:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.05_model.r WARNING @ Tue, 16 Jun 2020 09:27:32: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:32: #2 You may need to consider one of the other alternative d(s): 4,84,90 WARNING @ Tue, 16 Jun 2020 09:27:32: #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 09:27:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:35: 3000000 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 09:27:41: 4000000 INFO @ Tue, 16 Jun 2020 09:27:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.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 09:27:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:49: 5000000 INFO @ Tue, 16 Jun 2020 09:27:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:52: 1000000 INFO @ Tue, 16 Jun 2020 09:27:56: 6000000 INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.05_summits.bed INFO @ Tue, 16 Jun 2020 09:27:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4737 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:00: 2000000 INFO @ Tue, 16 Jun 2020 09:28:04: 7000000 INFO @ Tue, 16 Jun 2020 09:28:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:06: #1 total tags in treatment: 7226379 INFO @ Tue, 16 Jun 2020 09:28:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:06: #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 09:28:06: #1 tags after filtering in treatment: 7226379 INFO @ Tue, 16 Jun 2020 09:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:07: #2 number of paired peaks: 591 WARNING @ Tue, 16 Jun 2020 09:28:07: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:07: #2 predicted fragment length is 84 bps INFO @ Tue, 16 Jun 2020 09:28:07: #2 alternative fragment length(s) may be 4,84,90 bps INFO @ Tue, 16 Jun 2020 09:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.10_model.r WARNING @ Tue, 16 Jun 2020 09:28:07: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:07: #2 You may need to consider one of the other alternative d(s): 4,84,90 WARNING @ Tue, 16 Jun 2020 09:28:07: #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 09:28:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:08: 3000000 INFO @ Tue, 16 Jun 2020 09:28:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:23: 5000000 INFO @ Tue, 16 Jun 2020 09:28:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:30: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.10_summits.bed INFO @ Tue, 16 Jun 2020 09:28:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1253 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:38: 7000000 INFO @ Tue, 16 Jun 2020 09:28:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:39: #1 total tags in treatment: 7226379 INFO @ Tue, 16 Jun 2020 09:28:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:39: #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 09:28:39: #1 tags after filtering in treatment: 7226379 INFO @ Tue, 16 Jun 2020 09:28:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:40: #2 number of paired peaks: 591 WARNING @ Tue, 16 Jun 2020 09:28:40: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:40: #2 predicted fragment length is 84 bps INFO @ Tue, 16 Jun 2020 09:28:40: #2 alternative fragment length(s) may be 4,84,90 bps INFO @ Tue, 16 Jun 2020 09:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.20_model.r WARNING @ Tue, 16 Jun 2020 09:28:40: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:40: #2 You may need to consider one of the other alternative d(s): 4,84,90 WARNING @ Tue, 16 Jun 2020 09:28:40: #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 09:28:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466473/SRX466473.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling