Job ID = 6507987 SRX = SRX657409 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:28:32 prefetch.2.10.7: 1) Downloading 'SRR1520418'... 2020-06-26T13:28:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:29:59 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:30:00 prefetch.2.10.7: 'SRR1520418' is valid 2020-06-26T13:30:00 prefetch.2.10.7: 1) 'SRR1520418' was downloaded successfully Read 14817259 spots for SRR1520418/SRR1520418.sra Written 14817259 spots for SRR1520418/SRR1520418.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: 00:02:32 14817259 reads; of these: 14817259 (100.00%) were unpaired; of these: 2745678 (18.53%) aligned 0 times 10172287 (68.65%) aligned exactly 1 time 1899294 (12.82%) aligned >1 times 81.47% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 2797791 / 12071581 = 0.2318 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 @ Fri, 26 Jun 2020 22:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.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 @ Fri, 26 Jun 2020 22:36:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:25: 1000000 INFO @ Fri, 26 Jun 2020 22:36:30: 2000000 INFO @ Fri, 26 Jun 2020 22:36:34: 3000000 INFO @ Fri, 26 Jun 2020 22:36:39: 4000000 INFO @ Fri, 26 Jun 2020 22:36:44: 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 @ Fri, 26 Jun 2020 22:36:49: 6000000 INFO @ Fri, 26 Jun 2020 22:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.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 @ Fri, 26 Jun 2020 22:36:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:54: 7000000 INFO @ Fri, 26 Jun 2020 22:36:55: 1000000 INFO @ Fri, 26 Jun 2020 22:36:59: 8000000 INFO @ Fri, 26 Jun 2020 22:37:01: 2000000 INFO @ Fri, 26 Jun 2020 22:37:03: 9000000 INFO @ Fri, 26 Jun 2020 22:37:05: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 22:37:05: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 22:37:05: #1 total tags in treatment: 9273790 INFO @ Fri, 26 Jun 2020 22:37:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:37:05: #1 tags after filtering in treatment: 9273790 INFO @ Fri, 26 Jun 2020 22:37:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:05: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:06: #2 number of paired peaks: 571 WARNING @ Fri, 26 Jun 2020 22:37:06: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:06: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 22:37:06: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 26 Jun 2020 22:37:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.05_model.r INFO @ Fri, 26 Jun 2020 22:37:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:37:06: 3000000 INFO @ Fri, 26 Jun 2020 22:37:11: 4000000 INFO @ Fri, 26 Jun 2020 22:37:16: 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 @ Fri, 26 Jun 2020 22:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.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 @ Fri, 26 Jun 2020 22:37:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:22: 6000000 INFO @ Fri, 26 Jun 2020 22:37:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:37:27: 7000000 INFO @ Fri, 26 Jun 2020 22:37:28: 1000000 INFO @ Fri, 26 Jun 2020 22:37:33: 8000000 INFO @ Fri, 26 Jun 2020 22:37:35: 2000000 INFO @ Fri, 26 Jun 2020 22:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.05_summits.bed INFO @ Fri, 26 Jun 2020 22:37:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1896 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:37:38: 9000000 INFO @ Fri, 26 Jun 2020 22:37:40: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 22:37:40: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 22:37:40: #1 total tags in treatment: 9273790 INFO @ Fri, 26 Jun 2020 22:37:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:37:40: #1 tags after filtering in treatment: 9273790 INFO @ Fri, 26 Jun 2020 22:37:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:40: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:40: #2 number of paired peaks: 571 WARNING @ Fri, 26 Jun 2020 22:37:40: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:40: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:41: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:41: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:41: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:41: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 22:37:41: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 26 Jun 2020 22:37:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.10_model.r INFO @ Fri, 26 Jun 2020 22:37:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:37:41: 3000000 INFO @ Fri, 26 Jun 2020 22:37:47: 4000000 INFO @ Fri, 26 Jun 2020 22:37:53: 5000000 INFO @ Fri, 26 Jun 2020 22:37:58: 6000000 INFO @ Fri, 26 Jun 2020 22:38:01: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:38:04: 7000000 INFO @ Fri, 26 Jun 2020 22:38:09: 8000000 INFO @ Fri, 26 Jun 2020 22:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.10_summits.bed INFO @ Fri, 26 Jun 2020 22:38:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1191 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:38:15: 9000000 INFO @ Fri, 26 Jun 2020 22:38:16: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 22:38:16: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 22:38:16: #1 total tags in treatment: 9273790 INFO @ Fri, 26 Jun 2020 22:38:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:38:17: #1 tags after filtering in treatment: 9273790 INFO @ Fri, 26 Jun 2020 22:38:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:17: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:17: #2 number of paired peaks: 571 WARNING @ Fri, 26 Jun 2020 22:38:17: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:17: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:17: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:17: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:17: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:17: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 22:38:17: #2 alternative fragment length(s) may be 104 bps INFO @ Fri, 26 Jun 2020 22:38:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.20_model.r INFO @ Fri, 26 Jun 2020 22:38:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:38:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657409/SRX657409.20_summits.bed INFO @ Fri, 26 Jun 2020 22:38:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (661 records, 4 fields): 1 millis CompletedMACS2peakCalling