Job ID = 6366706 SRX = SRX2228861 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:52:11 prefetch.2.10.7: 1) Downloading 'SRR4380317'... 2020-06-15T22:52:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:15 prefetch.2.10.7: 'SRR4380317' is valid 2020-06-15T22:53:15 prefetch.2.10.7: 1) 'SRR4380317' was downloaded successfully Read 9436772 spots for SRR4380317/SRR4380317.sra Written 9436772 spots for SRR4380317/SRR4380317.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: 00:02:07 9436772 reads; of these: 9436772 (100.00%) were unpaired; of these: 566337 (6.00%) aligned 0 times 7378590 (78.19%) aligned exactly 1 time 1491845 (15.81%) aligned >1 times 94.00% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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_rmdupse_core] 794117 / 8870435 = 0.0895 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 07:58:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.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 07:58:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:53: 1000000 INFO @ Tue, 16 Jun 2020 07:58:59: 2000000 INFO @ Tue, 16 Jun 2020 07:59:06: 3000000 INFO @ Tue, 16 Jun 2020 07:59:13: 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 07:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.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 07:59:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:20: 5000000 INFO @ Tue, 16 Jun 2020 07:59:22: 1000000 INFO @ Tue, 16 Jun 2020 07:59:26: 6000000 INFO @ Tue, 16 Jun 2020 07:59:28: 2000000 INFO @ Tue, 16 Jun 2020 07:59:33: 7000000 INFO @ Tue, 16 Jun 2020 07:59:34: 3000000 INFO @ Tue, 16 Jun 2020 07:59:40: 4000000 INFO @ Tue, 16 Jun 2020 07:59:40: 8000000 INFO @ Tue, 16 Jun 2020 07:59:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:41: #1 total tags in treatment: 8076318 INFO @ Tue, 16 Jun 2020 07:59:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:41: #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 07:59:41: #1 tags after filtering in treatment: 8076318 INFO @ Tue, 16 Jun 2020 07:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:41: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:41: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 07:59:41: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:41: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:41: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:41: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:41: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:41: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 07:59:41: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 07:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.05_model.r INFO @ Tue, 16 Jun 2020 07:59:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:41: #3 Pre-compute pvalue-qvalue table... 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 07:59:46: 5000000 INFO @ Tue, 16 Jun 2020 07:59:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.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 07:59:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:51: 6000000 INFO @ Tue, 16 Jun 2020 07:59:52: 1000000 INFO @ Tue, 16 Jun 2020 07:59:57: 7000000 INFO @ Tue, 16 Jun 2020 07:59:58: 2000000 INFO @ Tue, 16 Jun 2020 07:59:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:03: 8000000 INFO @ Tue, 16 Jun 2020 08:00:04: 3000000 INFO @ Tue, 16 Jun 2020 08:00:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:04: #1 total tags in treatment: 8076318 INFO @ Tue, 16 Jun 2020 08:00:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:04: #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 08:00:04: #1 tags after filtering in treatment: 8076318 INFO @ Tue, 16 Jun 2020 08:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:04: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 08:00:04: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:04: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 08:00:04: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 08:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.10_model.r INFO @ Tue, 16 Jun 2020 08:00:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.05_summits.bed INFO @ Tue, 16 Jun 2020 08:00:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1328 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:09: 4000000 INFO @ Tue, 16 Jun 2020 08:00:15: 5000000 INFO @ Tue, 16 Jun 2020 08:00:21: 6000000 INFO @ Tue, 16 Jun 2020 08:00:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:26: 7000000 INFO @ Tue, 16 Jun 2020 08:00:32: 8000000 INFO @ Tue, 16 Jun 2020 08:00:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:32: #1 total tags in treatment: 8076318 INFO @ Tue, 16 Jun 2020 08:00:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:32: #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 08:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.10_summits.bed INFO @ Tue, 16 Jun 2020 08:00:32: Done! INFO @ Tue, 16 Jun 2020 08:00:32: #1 tags after filtering in treatment: 8076318 INFO @ Tue, 16 Jun 2020 08:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:32: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (716 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:33: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 08:00:33: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:33: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 08:00:33: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 08:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.20_model.r INFO @ Tue, 16 Jun 2020 08:00:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228861/SRX2228861.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (316 records, 4 fields): 2 millis CompletedMACS2peakCalling