Job ID = 6368114 SRX = SRX466577 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:52:03 prefetch.2.10.7: 1) Downloading 'SRR1163643'... 2020-06-15T23:52:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:43 prefetch.2.10.7: 'SRR1163643' is valid 2020-06-15T23:53:43 prefetch.2.10.7: 1) 'SRR1163643' was downloaded successfully Read 15863850 spots for SRR1163643/SRR1163643.sra Written 15863850 spots for SRR1163643/SRR1163643.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: 00:02:49 15863850 reads; of these: 15863850 (100.00%) were unpaired; of these: 231762 (1.46%) aligned 0 times 12990275 (81.89%) aligned exactly 1 time 2641813 (16.65%) aligned >1 times 98.54% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 1436640 / 15632088 = 0.0919 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 09:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.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 09:01:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:08: 1000000 INFO @ Tue, 16 Jun 2020 09:01:14: 2000000 INFO @ Tue, 16 Jun 2020 09:01:20: 3000000 INFO @ Tue, 16 Jun 2020 09:01:26: 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 09:01:32: 5000000 INFO @ Tue, 16 Jun 2020 09:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.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 09:01:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:38: 6000000 INFO @ Tue, 16 Jun 2020 09:01:38: 1000000 INFO @ Tue, 16 Jun 2020 09:01:45: 7000000 INFO @ Tue, 16 Jun 2020 09:01:45: 2000000 INFO @ Tue, 16 Jun 2020 09:01:51: 8000000 INFO @ Tue, 16 Jun 2020 09:01:51: 3000000 INFO @ Tue, 16 Jun 2020 09:01:58: 9000000 INFO @ Tue, 16 Jun 2020 09:01:58: 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 @ Tue, 16 Jun 2020 09:02:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.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 09:02:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:05: 10000000 INFO @ Tue, 16 Jun 2020 09:02:05: 5000000 INFO @ Tue, 16 Jun 2020 09:02:10: 1000000 INFO @ Tue, 16 Jun 2020 09:02:12: 11000000 INFO @ Tue, 16 Jun 2020 09:02:12: 6000000 INFO @ Tue, 16 Jun 2020 09:02:16: 2000000 INFO @ Tue, 16 Jun 2020 09:02:18: 12000000 INFO @ Tue, 16 Jun 2020 09:02:19: 7000000 INFO @ Tue, 16 Jun 2020 09:02:23: 3000000 INFO @ Tue, 16 Jun 2020 09:02:25: 13000000 INFO @ Tue, 16 Jun 2020 09:02:25: 8000000 INFO @ Tue, 16 Jun 2020 09:02:30: 4000000 INFO @ Tue, 16 Jun 2020 09:02:31: 14000000 INFO @ Tue, 16 Jun 2020 09:02:32: 9000000 INFO @ Tue, 16 Jun 2020 09:02:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:02:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:02:33: #1 total tags in treatment: 14195448 INFO @ Tue, 16 Jun 2020 09:02:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:33: #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 09:02:33: #1 tags after filtering in treatment: 14195448 INFO @ Tue, 16 Jun 2020 09:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:34: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 09:02:34: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:34: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:02:34: #2 alternative fragment length(s) may be 2,18,34,564 bps INFO @ Tue, 16 Jun 2020 09:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:34: #2 You may need to consider one of the other alternative d(s): 2,18,34,564 WARNING @ Tue, 16 Jun 2020 09:02:34: #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 09:02:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:36: 5000000 INFO @ Tue, 16 Jun 2020 09:02:39: 10000000 INFO @ Tue, 16 Jun 2020 09:02:43: 6000000 INFO @ Tue, 16 Jun 2020 09:02:45: 11000000 INFO @ Tue, 16 Jun 2020 09:02:49: 7000000 INFO @ Tue, 16 Jun 2020 09:02:52: 12000000 INFO @ Tue, 16 Jun 2020 09:02:56: 8000000 INFO @ Tue, 16 Jun 2020 09:02:58: 13000000 INFO @ Tue, 16 Jun 2020 09:02:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:02: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:05: 14000000 INFO @ Tue, 16 Jun 2020 09:03:07: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:03:07: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:03:07: #1 total tags in treatment: 14195448 INFO @ Tue, 16 Jun 2020 09:03:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:07: #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 09:03:07: #1 tags after filtering in treatment: 14195448 INFO @ Tue, 16 Jun 2020 09:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:08: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 09:03:08: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:08: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:03:08: #2 alternative fragment length(s) may be 2,18,34,564 bps INFO @ Tue, 16 Jun 2020 09:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.10_model.r WARNING @ Tue, 16 Jun 2020 09:03:08: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:08: #2 You may need to consider one of the other alternative d(s): 2,18,34,564 WARNING @ Tue, 16 Jun 2020 09:03:08: #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 09:03:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:09: 10000000 INFO @ Tue, 16 Jun 2020 09:03:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.05_summits.bed INFO @ Tue, 16 Jun 2020 09:03:11: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:15: 11000000 INFO @ Tue, 16 Jun 2020 09:03:21: 12000000 INFO @ Tue, 16 Jun 2020 09:03:27: 13000000 INFO @ Tue, 16 Jun 2020 09:03:33: 14000000 INFO @ Tue, 16 Jun 2020 09:03:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:34: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:03:34: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:03:34: #1 total tags in treatment: 14195448 INFO @ Tue, 16 Jun 2020 09:03:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:34: #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 09:03:34: #1 tags after filtering in treatment: 14195448 INFO @ Tue, 16 Jun 2020 09:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:35: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 09:03:35: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:35: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:03:35: #2 alternative fragment length(s) may be 2,18,34,564 bps INFO @ Tue, 16 Jun 2020 09:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:35: #2 You may need to consider one of the other alternative d(s): 2,18,34,564 WARNING @ Tue, 16 Jun 2020 09:03:35: #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 09:03:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466577/SRX466577.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:12: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling