Job ID = 6365832 SRX = ERX1999203 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:16:42 prefetch.2.10.7: 1) Downloading 'ERR1938670'... 2020-06-15T22:16:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:17:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:17:42 prefetch.2.10.7: 'ERR1938670' is valid 2020-06-15T22:17:42 prefetch.2.10.7: 1) 'ERR1938670' was downloaded successfully Read 12332550 spots for ERR1938670/ERR1938670.sra Written 12332550 spots for ERR1938670/ERR1938670.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: 00:03:20 12332550 reads; of these: 12332550 (100.00%) were unpaired; of these: 964718 (7.82%) aligned 0 times 6428542 (52.13%) aligned exactly 1 time 4939290 (40.05%) aligned >1 times 92.18% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 5674032 / 11367832 = 0.4991 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 07:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.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 07:24:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:21: 1000000 INFO @ Tue, 16 Jun 2020 07:24:27: 2000000 INFO @ Tue, 16 Jun 2020 07:24:33: 3000000 INFO @ Tue, 16 Jun 2020 07:24:40: 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 07:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.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 07:24:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:24:46: 5000000 INFO @ Tue, 16 Jun 2020 07:24:51: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:24:51: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:24:51: #1 total tags in treatment: 5693800 INFO @ Tue, 16 Jun 2020 07:24:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:24:51: #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 07:24:51: #1 tags after filtering in treatment: 5693800 INFO @ Tue, 16 Jun 2020 07:24:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:24:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:24:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:24:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:24:51: #2 number of paired peaks: 4495 INFO @ Tue, 16 Jun 2020 07:24:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:24:51: start X-correlation... INFO @ Tue, 16 Jun 2020 07:24:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:24:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:24:51: #2 predicted fragment length is 3 bps INFO @ Tue, 16 Jun 2020 07:24:51: #2 alternative fragment length(s) may be 3,13,59,83 bps INFO @ Tue, 16 Jun 2020 07:24:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.05_model.r WARNING @ Tue, 16 Jun 2020 07:24:51: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:24:51: #2 You may need to consider one of the other alternative d(s): 3,13,59,83 WARNING @ Tue, 16 Jun 2020 07:24:51: #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 07:24:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:24:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:24:52: 1000000 INFO @ Tue, 16 Jun 2020 07:24:58: 2000000 INFO @ Tue, 16 Jun 2020 07:25:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:04: 3000000 INFO @ Tue, 16 Jun 2020 07:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.05_summits.bed INFO @ Tue, 16 Jun 2020 07:25:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:25:10: 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 07:25:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.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 07:25:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:16: 5000000 INFO @ Tue, 16 Jun 2020 07:25:20: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:25:20: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:25:20: #1 total tags in treatment: 5693800 INFO @ Tue, 16 Jun 2020 07:25:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:20: #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 07:25:21: #1 tags after filtering in treatment: 5693800 INFO @ Tue, 16 Jun 2020 07:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:21: 1000000 INFO @ Tue, 16 Jun 2020 07:25:21: #2 number of paired peaks: 4495 INFO @ Tue, 16 Jun 2020 07:25:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:21: #2 predicted fragment length is 3 bps INFO @ Tue, 16 Jun 2020 07:25:21: #2 alternative fragment length(s) may be 3,13,59,83 bps INFO @ Tue, 16 Jun 2020 07:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.10_model.r WARNING @ Tue, 16 Jun 2020 07:25:21: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:25:21: #2 You may need to consider one of the other alternative d(s): 3,13,59,83 WARNING @ Tue, 16 Jun 2020 07:25:21: #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 07:25:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:25:27: 2000000 INFO @ Tue, 16 Jun 2020 07:25:33: 3000000 INFO @ Tue, 16 Jun 2020 07:25:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:40: 4000000 INFO @ Tue, 16 Jun 2020 07:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.10_summits.bed INFO @ Tue, 16 Jun 2020 07:25:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:25:46: 5000000 INFO @ Tue, 16 Jun 2020 07:25:50: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:25:50: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:25:50: #1 total tags in treatment: 5693800 INFO @ Tue, 16 Jun 2020 07:25:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:50: #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 07:25:50: #1 tags after filtering in treatment: 5693800 INFO @ Tue, 16 Jun 2020 07:25:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:50: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:51: #2 number of paired peaks: 4495 INFO @ Tue, 16 Jun 2020 07:25:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:51: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:51: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:51: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:51: #2 predicted fragment length is 3 bps INFO @ Tue, 16 Jun 2020 07:25:51: #2 alternative fragment length(s) may be 3,13,59,83 bps INFO @ Tue, 16 Jun 2020 07:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.20_model.r WARNING @ Tue, 16 Jun 2020 07:25:51: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:25:51: #2 You may need to consider one of the other alternative d(s): 3,13,59,83 WARNING @ Tue, 16 Jun 2020 07:25:51: #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 07:25:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:26:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999203/ERX1999203.20_summits.bed INFO @ Tue, 16 Jun 2020 07:26:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling