Job ID = 6365826 SRX = ERX1999197 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:21 prefetch.2.10.7: 1) Downloading 'ERR1938664'... 2020-06-15T22:37:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:38 prefetch.2.10.7: 'ERR1938664' is valid 2020-06-15T22:38:38 prefetch.2.10.7: 1) 'ERR1938664' was downloaded successfully Read 15214017 spots for ERR1938664/ERR1938664.sra Written 15214017 spots for ERR1938664/ERR1938664.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:18 15214017 reads; of these: 15214017 (100.00%) were unpaired; of these: 339608 (2.23%) aligned 0 times 9446474 (62.09%) aligned exactly 1 time 5427935 (35.68%) aligned >1 times 97.77% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 6264141 / 14874409 = 0.4211 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 07:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.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 07:47:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:47:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:47:38: 1000000 INFO @ Tue, 16 Jun 2020 07:47:44: 2000000 INFO @ Tue, 16 Jun 2020 07:47:49: 3000000 INFO @ Tue, 16 Jun 2020 07:47:55: 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 07:48:01: 5000000 INFO @ Tue, 16 Jun 2020 07:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.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 07:48:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:06: 6000000 INFO @ Tue, 16 Jun 2020 07:48:09: 1000000 INFO @ Tue, 16 Jun 2020 07:48:12: 7000000 INFO @ Tue, 16 Jun 2020 07:48:16: 2000000 INFO @ Tue, 16 Jun 2020 07:48:18: 8000000 INFO @ Tue, 16 Jun 2020 07:48:22: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:48:22: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:48:22: #1 total tags in treatment: 8610268 INFO @ Tue, 16 Jun 2020 07:48:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:22: #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 07:48:22: #1 tags after filtering in treatment: 8610268 INFO @ Tue, 16 Jun 2020 07:48:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:48:22: 3000000 INFO @ Tue, 16 Jun 2020 07:48:23: #2 number of paired peaks: 2533 INFO @ Tue, 16 Jun 2020 07:48:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:48:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:48:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:48:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:48:23: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 07:48:23: #2 alternative fragment length(s) may be 2,53,70,131 bps INFO @ Tue, 16 Jun 2020 07:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.05_model.r WARNING @ Tue, 16 Jun 2020 07:48:23: #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 07:48:23: #2 You may need to consider one of the other alternative d(s): 2,53,70,131 WARNING @ Tue, 16 Jun 2020 07:48:23: #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 07:48:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:48:29: 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 07:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.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 07:48:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:35: 5000000 INFO @ Tue, 16 Jun 2020 07:48:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:39: 1000000 INFO @ Tue, 16 Jun 2020 07:48:42: 6000000 INFO @ Tue, 16 Jun 2020 07:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.05_summits.bed INFO @ Tue, 16 Jun 2020 07:48:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:48:45: 2000000 INFO @ Tue, 16 Jun 2020 07:48:48: 7000000 INFO @ Tue, 16 Jun 2020 07:48:51: 3000000 INFO @ Tue, 16 Jun 2020 07:48:55: 8000000 INFO @ Tue, 16 Jun 2020 07:48:57: 4000000 INFO @ Tue, 16 Jun 2020 07:48:59: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:48:59: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:48:59: #1 total tags in treatment: 8610268 INFO @ Tue, 16 Jun 2020 07:48:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:48:59: #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 07:48:59: #1 tags after filtering in treatment: 8610268 INFO @ Tue, 16 Jun 2020 07:48:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:48:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:48:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:00: #2 number of paired peaks: 2533 INFO @ Tue, 16 Jun 2020 07:49:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:00: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 07:49:00: #2 alternative fragment length(s) may be 2,53,70,131 bps INFO @ Tue, 16 Jun 2020 07:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.10_model.r WARNING @ Tue, 16 Jun 2020 07:49:00: #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 07:49:00: #2 You may need to consider one of the other alternative d(s): 2,53,70,131 WARNING @ Tue, 16 Jun 2020 07:49:00: #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 07:49:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:03: 5000000 INFO @ Tue, 16 Jun 2020 07:49:09: 6000000 INFO @ Tue, 16 Jun 2020 07:49:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:14: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:49:20: 8000000 INFO @ Tue, 16 Jun 2020 07:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.10_summits.bed INFO @ Tue, 16 Jun 2020 07:49:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:49:23: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:49:23: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:49:23: #1 total tags in treatment: 8610268 INFO @ Tue, 16 Jun 2020 07:49:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:23: #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 07:49:23: #1 tags after filtering in treatment: 8610268 INFO @ Tue, 16 Jun 2020 07:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:23: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:24: #2 number of paired peaks: 2533 INFO @ Tue, 16 Jun 2020 07:49:24: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:24: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:24: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:24: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:24: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 07:49:24: #2 alternative fragment length(s) may be 2,53,70,131 bps INFO @ Tue, 16 Jun 2020 07:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.20_model.r WARNING @ Tue, 16 Jun 2020 07:49:24: #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 07:49:24: #2 You may need to consider one of the other alternative d(s): 2,53,70,131 WARNING @ Tue, 16 Jun 2020 07:49:24: #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 07:49:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:49:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999197/ERX1999197.20_summits.bed INFO @ Tue, 16 Jun 2020 07:49:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling