Job ID = 6368396 SRX = SRX495075 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:46 prefetch.2.10.7: 1) Downloading 'SRR1198607'... 2020-06-16T00:26:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:59 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:59 prefetch.2.10.7: 'SRR1198607' is valid 2020-06-16T00:28:59 prefetch.2.10.7: 1) 'SRR1198607' was downloaded successfully Read 12762765 spots for SRR1198607/SRR1198607.sra Written 12762765 spots for SRR1198607/SRR1198607.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: 00:02:27 12762765 reads; of these: 12762765 (100.00%) were unpaired; of these: 981015 (7.69%) aligned 0 times 9881794 (77.43%) aligned exactly 1 time 1899956 (14.89%) aligned >1 times 92.31% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 3868794 / 11781750 = 0.3284 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 09:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.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 09:35:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:36: 1000000 INFO @ Tue, 16 Jun 2020 09:35:43: 2000000 INFO @ Tue, 16 Jun 2020 09:35:49: 3000000 INFO @ Tue, 16 Jun 2020 09:35:56: 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 09:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.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 09:36:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:02: 5000000 INFO @ Tue, 16 Jun 2020 09:36:07: 1000000 INFO @ Tue, 16 Jun 2020 09:36:08: 6000000 INFO @ Tue, 16 Jun 2020 09:36:14: 2000000 INFO @ Tue, 16 Jun 2020 09:36:15: 7000000 INFO @ Tue, 16 Jun 2020 09:36:20: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:36:20: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:36:20: #1 total tags in treatment: 7912956 INFO @ Tue, 16 Jun 2020 09:36:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:20: #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 09:36:21: #1 tags after filtering in treatment: 7912956 INFO @ Tue, 16 Jun 2020 09:36:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:21: 3000000 INFO @ Tue, 16 Jun 2020 09:36:21: #2 number of paired peaks: 540 WARNING @ Tue, 16 Jun 2020 09:36:21: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:21: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 09:36:21: #2 alternative fragment length(s) may be 4,127 bps INFO @ Tue, 16 Jun 2020 09:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.05_model.r INFO @ Tue, 16 Jun 2020 09:36:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:28: 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 09:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.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 09:36:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:35: 5000000 INFO @ Tue, 16 Jun 2020 09:36:37: 1000000 INFO @ Tue, 16 Jun 2020 09:36:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:42: 6000000 INFO @ Tue, 16 Jun 2020 09:36:44: 2000000 INFO @ Tue, 16 Jun 2020 09:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1561 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:48: 7000000 INFO @ Tue, 16 Jun 2020 09:36:50: 3000000 INFO @ Tue, 16 Jun 2020 09:36:54: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:36:54: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:36:54: #1 total tags in treatment: 7912956 INFO @ Tue, 16 Jun 2020 09:36:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:55: #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 09:36:55: #1 tags after filtering in treatment: 7912956 INFO @ Tue, 16 Jun 2020 09:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:55: #2 number of paired peaks: 540 WARNING @ Tue, 16 Jun 2020 09:36:55: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:55: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 09:36:55: #2 alternative fragment length(s) may be 4,127 bps INFO @ Tue, 16 Jun 2020 09:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.10_model.r INFO @ Tue, 16 Jun 2020 09:36:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:57: 4000000 INFO @ Tue, 16 Jun 2020 09:37:03: 5000000 INFO @ Tue, 16 Jun 2020 09:37:10: 6000000 INFO @ Tue, 16 Jun 2020 09:37:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:16: 7000000 INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (857 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:37:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:37:22: #1 total tags in treatment: 7912956 INFO @ Tue, 16 Jun 2020 09:37:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:22: #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 09:37:22: #1 tags after filtering in treatment: 7912956 INFO @ Tue, 16 Jun 2020 09:37:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:23: #2 number of paired peaks: 540 WARNING @ Tue, 16 Jun 2020 09:37:23: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:23: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 09:37:23: #2 alternative fragment length(s) may be 4,127 bps INFO @ Tue, 16 Jun 2020 09:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.20_model.r INFO @ Tue, 16 Jun 2020 09:37:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495075/SRX495075.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling