Job ID = 6368192 SRX = SRX494876 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:50 prefetch.2.10.7: 1) Downloading 'SRR1198408'... 2020-06-15T23:58:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:47 prefetch.2.10.7: 1) 'SRR1198408' was downloaded successfully Read 18388946 spots for SRR1198408/SRR1198408.sra Written 18388946 spots for SRR1198408/SRR1198408.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: 00:03:30 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337272 (23.59%) aligned 0 times 11667991 (63.45%) aligned exactly 1 time 2383683 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1117629 / 14051674 = 0.0795 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 09:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.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 09:08:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:52: 1000000 INFO @ Tue, 16 Jun 2020 09:08:58: 2000000 INFO @ Tue, 16 Jun 2020 09:09:03: 3000000 INFO @ Tue, 16 Jun 2020 09:09:08: 4000000 INFO @ Tue, 16 Jun 2020 09:09:13: 5000000 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 09:09:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.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 09:09:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:19: 6000000 INFO @ Tue, 16 Jun 2020 09:09:24: 1000000 INFO @ Tue, 16 Jun 2020 09:09:24: 7000000 INFO @ Tue, 16 Jun 2020 09:09:30: 8000000 INFO @ Tue, 16 Jun 2020 09:09:31: 2000000 INFO @ Tue, 16 Jun 2020 09:09:36: 9000000 INFO @ Tue, 16 Jun 2020 09:09:37: 3000000 INFO @ Tue, 16 Jun 2020 09:09:42: 10000000 INFO @ Tue, 16 Jun 2020 09:09:44: 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 09:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.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 09:09:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:48: 11000000 INFO @ Tue, 16 Jun 2020 09:09:51: 5000000 INFO @ Tue, 16 Jun 2020 09:09:54: 1000000 INFO @ Tue, 16 Jun 2020 09:09:54: 12000000 INFO @ Tue, 16 Jun 2020 09:09:58: 6000000 INFO @ Tue, 16 Jun 2020 09:10:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:00: #1 total tags in treatment: 12934045 INFO @ Tue, 16 Jun 2020 09:10:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:00: #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 09:10:00: #1 tags after filtering in treatment: 12934045 INFO @ Tue, 16 Jun 2020 09:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:00: 2000000 INFO @ Tue, 16 Jun 2020 09:10:01: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 09:10:01: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:01: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:10:01: #2 alternative fragment length(s) may be 1,40,532,556 bps INFO @ Tue, 16 Jun 2020 09:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:01: #2 You may need to consider one of the other alternative d(s): 1,40,532,556 WARNING @ Tue, 16 Jun 2020 09:10:01: #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 09:10:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:05: 7000000 INFO @ Tue, 16 Jun 2020 09:10:07: 3000000 INFO @ Tue, 16 Jun 2020 09:10:12: 8000000 INFO @ Tue, 16 Jun 2020 09:10:14: 4000000 INFO @ Tue, 16 Jun 2020 09:10:18: 9000000 INFO @ Tue, 16 Jun 2020 09:10:20: 5000000 INFO @ Tue, 16 Jun 2020 09:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:25: 10000000 INFO @ Tue, 16 Jun 2020 09:10:27: 6000000 INFO @ Tue, 16 Jun 2020 09:10:32: 11000000 INFO @ Tue, 16 Jun 2020 09:10:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:34: 7000000 INFO @ Tue, 16 Jun 2020 09:10:39: 12000000 INFO @ Tue, 16 Jun 2020 09:10:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:45: #1 total tags in treatment: 12934045 INFO @ Tue, 16 Jun 2020 09:10:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:45: #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 09:10:45: #1 tags after filtering in treatment: 12934045 INFO @ Tue, 16 Jun 2020 09:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:46: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 09:10:46: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:46: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:10:46: #2 alternative fragment length(s) may be 1,40,532,556 bps INFO @ Tue, 16 Jun 2020 09:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:46: #2 You may need to consider one of the other alternative d(s): 1,40,532,556 WARNING @ Tue, 16 Jun 2020 09:10:46: #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 09:10:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:47: 9000000 INFO @ Tue, 16 Jun 2020 09:10:53: 10000000 INFO @ Tue, 16 Jun 2020 09:10:59: 11000000 INFO @ Tue, 16 Jun 2020 09:11:06: 12000000 INFO @ Tue, 16 Jun 2020 09:11:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:11: #1 total tags in treatment: 12934045 INFO @ Tue, 16 Jun 2020 09:11:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:11: #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 09:11:12: #1 tags after filtering in treatment: 12934045 INFO @ Tue, 16 Jun 2020 09:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:13: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 09:11:13: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:13: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:11:13: #2 alternative fragment length(s) may be 1,40,532,556 bps INFO @ Tue, 16 Jun 2020 09:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:13: #2 You may need to consider one of the other alternative d(s): 1,40,532,556 WARNING @ Tue, 16 Jun 2020 09:11:13: #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 09:11:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:19: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494876/SRX494876.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling