Job ID = 6368233 SRX = SRX494916 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:59:05 prefetch.2.10.7: 1) Downloading 'SRR1198448'... 2020-06-15T23:59:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:17 prefetch.2.10.7: 1) 'SRR1198448' was downloaded successfully Read 26877758 spots for SRR1198448/SRR1198448.sra Written 26877758 spots for SRR1198448/SRR1198448.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: 00:06:10 26877758 reads; of these: 26877758 (100.00%) were unpaired; of these: 1662157 (6.18%) aligned 0 times 20503409 (76.28%) aligned exactly 1 time 4712192 (17.53%) aligned >1 times 93.82% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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 12 files... [bam_rmdupse_core] 7478988 / 25215601 = 0.2966 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 09:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.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 09:14:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:47: 1000000 INFO @ Tue, 16 Jun 2020 09:14:54: 2000000 INFO @ Tue, 16 Jun 2020 09:15:00: 3000000 INFO @ Tue, 16 Jun 2020 09:15:06: 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 09:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.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 09:15:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:13: 5000000 INFO @ Tue, 16 Jun 2020 09:15:17: 1000000 INFO @ Tue, 16 Jun 2020 09:15:20: 6000000 INFO @ Tue, 16 Jun 2020 09:15:24: 2000000 INFO @ Tue, 16 Jun 2020 09:15:27: 7000000 INFO @ Tue, 16 Jun 2020 09:15:30: 3000000 INFO @ Tue, 16 Jun 2020 09:15:34: 8000000 INFO @ Tue, 16 Jun 2020 09:15:37: 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 09:15:40: 9000000 INFO @ Tue, 16 Jun 2020 09:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.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 09:15:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:43: 5000000 INFO @ Tue, 16 Jun 2020 09:15:47: 10000000 INFO @ Tue, 16 Jun 2020 09:15:48: 1000000 INFO @ Tue, 16 Jun 2020 09:15:50: 6000000 INFO @ Tue, 16 Jun 2020 09:15:54: 11000000 INFO @ Tue, 16 Jun 2020 09:15:55: 2000000 INFO @ Tue, 16 Jun 2020 09:15:56: 7000000 INFO @ Tue, 16 Jun 2020 09:16:02: 12000000 INFO @ Tue, 16 Jun 2020 09:16:02: 3000000 INFO @ Tue, 16 Jun 2020 09:16:03: 8000000 INFO @ Tue, 16 Jun 2020 09:16:09: 13000000 INFO @ Tue, 16 Jun 2020 09:16:09: 4000000 INFO @ Tue, 16 Jun 2020 09:16:10: 9000000 INFO @ Tue, 16 Jun 2020 09:16:16: 14000000 INFO @ Tue, 16 Jun 2020 09:16:16: 5000000 INFO @ Tue, 16 Jun 2020 09:16:16: 10000000 INFO @ Tue, 16 Jun 2020 09:16:23: 15000000 INFO @ Tue, 16 Jun 2020 09:16:23: 11000000 INFO @ Tue, 16 Jun 2020 09:16:23: 6000000 INFO @ Tue, 16 Jun 2020 09:16:30: 12000000 INFO @ Tue, 16 Jun 2020 09:16:30: 16000000 INFO @ Tue, 16 Jun 2020 09:16:30: 7000000 INFO @ Tue, 16 Jun 2020 09:16:36: 13000000 INFO @ Tue, 16 Jun 2020 09:16:36: 17000000 INFO @ Tue, 16 Jun 2020 09:16:37: 8000000 INFO @ Tue, 16 Jun 2020 09:16:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:41: #1 total tags in treatment: 17736613 INFO @ Tue, 16 Jun 2020 09:16:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:41: #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 09:16:42: #1 tags after filtering in treatment: 17736613 INFO @ Tue, 16 Jun 2020 09:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:43: 14000000 INFO @ Tue, 16 Jun 2020 09:16:43: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 09:16:43: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:16:43: #2 alternative fragment length(s) may be 1,17,46,551,560,597 bps INFO @ Tue, 16 Jun 2020 09:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:43: #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 09:16:43: #2 You may need to consider one of the other alternative d(s): 1,17,46,551,560,597 WARNING @ Tue, 16 Jun 2020 09:16:43: #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 09:16:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:44: 9000000 INFO @ Tue, 16 Jun 2020 09:16:49: 15000000 INFO @ Tue, 16 Jun 2020 09:16:51: 10000000 INFO @ Tue, 16 Jun 2020 09:16:56: 16000000 INFO @ Tue, 16 Jun 2020 09:16:57: 11000000 INFO @ Tue, 16 Jun 2020 09:17:02: 17000000 INFO @ Tue, 16 Jun 2020 09:17:05: 12000000 INFO @ Tue, 16 Jun 2020 09:17:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:17:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:17:07: #1 total tags in treatment: 17736613 INFO @ Tue, 16 Jun 2020 09:17:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:07: #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 09:17:08: #1 tags after filtering in treatment: 17736613 INFO @ Tue, 16 Jun 2020 09:17:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:09: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 09:17:09: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:09: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:17:09: #2 alternative fragment length(s) may be 1,17,46,551,560,597 bps INFO @ Tue, 16 Jun 2020 09:17:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:09: #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 09:17:09: #2 You may need to consider one of the other alternative d(s): 1,17,46,551,560,597 WARNING @ Tue, 16 Jun 2020 09:17:09: #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 09:17:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:11: 13000000 INFO @ Tue, 16 Jun 2020 09:17:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:18: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:24: 15000000 INFO @ Tue, 16 Jun 2020 09:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:30: 16000000 INFO @ Tue, 16 Jun 2020 09:17:37: 17000000 INFO @ Tue, 16 Jun 2020 09:17:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:17:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:17:41: #1 total tags in treatment: 17736613 INFO @ Tue, 16 Jun 2020 09:17:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:41: #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 09:17:42: #1 tags after filtering in treatment: 17736613 INFO @ Tue, 16 Jun 2020 09:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:43: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 09:17:43: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:17:43: #2 alternative fragment length(s) may be 1,17,46,551,560,597 bps INFO @ Tue, 16 Jun 2020 09:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:43: #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 09:17:43: #2 You may need to consider one of the other alternative d(s): 1,17,46,551,560,597 WARNING @ Tue, 16 Jun 2020 09:17:43: #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 09:17:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494916/SRX494916.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling