Job ID = 6368379 SRX = SRX495059 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:19:21 prefetch.2.10.7: 1) Downloading 'SRR1198591'... 2020-06-16T00:19:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:04 prefetch.2.10.7: 'SRR1198591' is valid 2020-06-16T00:21:04 prefetch.2.10.7: 1) 'SRR1198591' was downloaded successfully Read 12994743 spots for SRR1198591/SRR1198591.sra Written 12994743 spots for SRR1198591/SRR1198591.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: 00:02:19 12994743 reads; of these: 12994743 (100.00%) were unpaired; of these: 702701 (5.41%) aligned 0 times 10231480 (78.74%) aligned exactly 1 time 2060562 (15.86%) aligned >1 times 94.59% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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_rmdupse_core] 4005444 / 12292042 = 0.3259 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 09:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.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 09:27:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:06: 1000000 INFO @ Tue, 16 Jun 2020 09:27:12: 2000000 INFO @ Tue, 16 Jun 2020 09:27:17: 3000000 INFO @ Tue, 16 Jun 2020 09:27:23: 4000000 INFO @ Tue, 16 Jun 2020 09:27:29: 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 @ Tue, 16 Jun 2020 09:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.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 09:27:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:34: 6000000 INFO @ Tue, 16 Jun 2020 09:27:36: 1000000 INFO @ Tue, 16 Jun 2020 09:27:40: 7000000 INFO @ Tue, 16 Jun 2020 09:27:42: 2000000 INFO @ Tue, 16 Jun 2020 09:27:46: 8000000 INFO @ Tue, 16 Jun 2020 09:27:47: 3000000 INFO @ Tue, 16 Jun 2020 09:27:47: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:27:47: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:27:47: #1 total tags in treatment: 8286598 INFO @ Tue, 16 Jun 2020 09:27:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:47: #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 09:27:48: #1 tags after filtering in treatment: 8286598 INFO @ Tue, 16 Jun 2020 09:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:48: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:27:48: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:48: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 09:27:48: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 16 Jun 2020 09:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.05_model.r INFO @ Tue, 16 Jun 2020 09:27:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:52: 4000000 INFO @ Tue, 16 Jun 2020 09:27:57: 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 @ Tue, 16 Jun 2020 09:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.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 09:28:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:03: 6000000 INFO @ Tue, 16 Jun 2020 09:28:07: 1000000 INFO @ Tue, 16 Jun 2020 09:28:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:08: 7000000 INFO @ Tue, 16 Jun 2020 09:28:13: 2000000 INFO @ Tue, 16 Jun 2020 09:28:13: 8000000 INFO @ Tue, 16 Jun 2020 09:28:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:28:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:28:15: #1 total tags in treatment: 8286598 INFO @ Tue, 16 Jun 2020 09:28:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:15: #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 09:28:15: #1 tags after filtering in treatment: 8286598 INFO @ Tue, 16 Jun 2020 09:28:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:15: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:28:15: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:15: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 09:28:15: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 16 Jun 2020 09:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.10_model.r INFO @ Tue, 16 Jun 2020 09:28:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1829 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:18: 3000000 INFO @ Tue, 16 Jun 2020 09:28:24: 4000000 INFO @ Tue, 16 Jun 2020 09:28:30: 5000000 INFO @ Tue, 16 Jun 2020 09:28:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:36: 6000000 INFO @ Tue, 16 Jun 2020 09:28:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.10_summits.bed INFO @ Tue, 16 Jun 2020 09:28:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (968 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:47: 8000000 INFO @ Tue, 16 Jun 2020 09:28:48: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:28:48: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:28:48: #1 total tags in treatment: 8286598 INFO @ Tue, 16 Jun 2020 09:28:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:48: #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 09:28:49: #1 tags after filtering in treatment: 8286598 INFO @ Tue, 16 Jun 2020 09:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:49: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:28:49: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:49: #2 predicted fragment length is 125 bps INFO @ Tue, 16 Jun 2020 09:28:49: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 16 Jun 2020 09:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.20_model.r INFO @ Tue, 16 Jun 2020 09:28:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495059/SRX495059.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 1 millis CompletedMACS2peakCalling