Job ID = 6365835 SRX = ERX1999206 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:28:59 prefetch.2.10.7: 1) Downloading 'ERR1938673'... 2020-06-15T22:28:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:46 prefetch.2.10.7: 1) 'ERR1938673' was downloaded successfully Read 24237636 spots for ERR1938673/ERR1938673.sra Written 24237636 spots for ERR1938673/ERR1938673.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: 00:05:42 24237636 reads; of these: 24237636 (100.00%) were unpaired; of these: 635641 (2.62%) aligned 0 times 18011894 (74.31%) aligned exactly 1 time 5590101 (23.06%) aligned >1 times 97.38% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 10608942 / 23601995 = 0.4495 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 07:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.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 07:42:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:22: 1000000 INFO @ Tue, 16 Jun 2020 07:42:26: 2000000 INFO @ Tue, 16 Jun 2020 07:42:31: 3000000 INFO @ Tue, 16 Jun 2020 07:42:36: 4000000 INFO @ Tue, 16 Jun 2020 07:42:41: 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 07:42:46: 6000000 INFO @ Tue, 16 Jun 2020 07:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.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 07:42:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:51: 7000000 INFO @ Tue, 16 Jun 2020 07:42:52: 1000000 INFO @ Tue, 16 Jun 2020 07:42:57: 8000000 INFO @ Tue, 16 Jun 2020 07:42:57: 2000000 INFO @ Tue, 16 Jun 2020 07:43:02: 9000000 INFO @ Tue, 16 Jun 2020 07:43:02: 3000000 INFO @ Tue, 16 Jun 2020 07:43:07: 10000000 INFO @ Tue, 16 Jun 2020 07:43:07: 4000000 INFO @ Tue, 16 Jun 2020 07:43:12: 11000000 INFO @ Tue, 16 Jun 2020 07:43:12: 5000000 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 07:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.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 07:43:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:18: 12000000 INFO @ Tue, 16 Jun 2020 07:43:18: 6000000 INFO @ Tue, 16 Jun 2020 07:43:22: 1000000 INFO @ Tue, 16 Jun 2020 07:43:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:23: #1 total tags in treatment: 12993053 INFO @ Tue, 16 Jun 2020 07:43:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:23: #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 07:43:23: #1 tags after filtering in treatment: 12993053 INFO @ Tue, 16 Jun 2020 07:43:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:23: 7000000 INFO @ Tue, 16 Jun 2020 07:43:24: #2 number of paired peaks: 177 WARNING @ Tue, 16 Jun 2020 07:43:24: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:24: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 07:43:24: #2 alternative fragment length(s) may be 2,32,52,473 bps INFO @ Tue, 16 Jun 2020 07:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.05_model.r WARNING @ Tue, 16 Jun 2020 07:43:24: #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 07:43:24: #2 You may need to consider one of the other alternative d(s): 2,32,52,473 WARNING @ Tue, 16 Jun 2020 07:43:24: #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 07:43:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:27: 2000000 INFO @ Tue, 16 Jun 2020 07:43:28: 8000000 INFO @ Tue, 16 Jun 2020 07:43:33: 3000000 INFO @ Tue, 16 Jun 2020 07:43:34: 9000000 INFO @ Tue, 16 Jun 2020 07:43:38: 4000000 INFO @ Tue, 16 Jun 2020 07:43:39: 10000000 INFO @ Tue, 16 Jun 2020 07:43:44: 5000000 INFO @ Tue, 16 Jun 2020 07:43:44: 11000000 INFO @ Tue, 16 Jun 2020 07:43:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:49: 6000000 INFO @ Tue, 16 Jun 2020 07:43:50: 12000000 INFO @ Tue, 16 Jun 2020 07:43:55: 7000000 INFO @ Tue, 16 Jun 2020 07:43:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:55: #1 total tags in treatment: 12993053 INFO @ Tue, 16 Jun 2020 07:43:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:55: #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 07:43:56: #1 tags after filtering in treatment: 12993053 INFO @ Tue, 16 Jun 2020 07:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:56: #2 number of paired peaks: 177 WARNING @ Tue, 16 Jun 2020 07:43:56: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:57: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 07:43:57: #2 alternative fragment length(s) may be 2,32,52,473 bps INFO @ Tue, 16 Jun 2020 07:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.10_model.r WARNING @ Tue, 16 Jun 2020 07:43:57: #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 07:43:57: #2 You may need to consider one of the other alternative d(s): 2,32,52,473 WARNING @ Tue, 16 Jun 2020 07:43:57: #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 07:43:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:00: 8000000 INFO @ Tue, 16 Jun 2020 07:44:05: 9000000 INFO @ Tue, 16 Jun 2020 07:44:11: 10000000 INFO @ Tue, 16 Jun 2020 07:44:16: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:21: 12000000 INFO @ Tue, 16 Jun 2020 07:44:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:26: #1 total tags in treatment: 12993053 INFO @ Tue, 16 Jun 2020 07:44:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:26: #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 07:44:26: #1 tags after filtering in treatment: 12993053 INFO @ Tue, 16 Jun 2020 07:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:27: #2 number of paired peaks: 177 WARNING @ Tue, 16 Jun 2020 07:44:27: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:28: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 07:44:28: #2 alternative fragment length(s) may be 2,32,52,473 bps INFO @ Tue, 16 Jun 2020 07:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.20_model.r WARNING @ Tue, 16 Jun 2020 07:44:28: #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 07:44:28: #2 You may need to consider one of the other alternative d(s): 2,32,52,473 WARNING @ Tue, 16 Jun 2020 07:44:28: #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 07:44:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:30: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999206/ERX1999206.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling