Job ID = 6368816 SRX = SRX5985670 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:36:20 prefetch.2.10.7: 1) Downloading 'SRR9214975'... 2020-06-16T00:36:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:52 prefetch.2.10.7: 1) 'SRR9214975' was downloaded successfully Read 29916745 spots for SRR9214975/SRR9214975.sra Written 29916745 spots for SRR9214975/SRR9214975.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: 00:09:11 29916745 reads; of these: 29916745 (100.00%) were unpaired; of these: 794913 (2.66%) aligned 0 times 26154589 (87.42%) aligned exactly 1 time 2967243 (9.92%) aligned >1 times 97.34% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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 12 files... [bam_rmdupse_core] 6403399 / 29121832 = 0.2199 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 09:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.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 09:59:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:09: 1000000 INFO @ Tue, 16 Jun 2020 09:59:15: 2000000 INFO @ Tue, 16 Jun 2020 09:59:22: 3000000 INFO @ Tue, 16 Jun 2020 09:59:29: 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 09:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.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 09:59:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:36: 5000000 INFO @ Tue, 16 Jun 2020 09:59:38: 1000000 INFO @ Tue, 16 Jun 2020 09:59:43: 6000000 INFO @ Tue, 16 Jun 2020 09:59:45: 2000000 INFO @ Tue, 16 Jun 2020 09:59:50: 7000000 INFO @ Tue, 16 Jun 2020 09:59:52: 3000000 INFO @ Tue, 16 Jun 2020 09:59:58: 8000000 INFO @ Tue, 16 Jun 2020 09:59:59: 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 10:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.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 10:00:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:05: 9000000 INFO @ Tue, 16 Jun 2020 10:00:06: 5000000 INFO @ Tue, 16 Jun 2020 10:00:08: 1000000 INFO @ Tue, 16 Jun 2020 10:00:12: 10000000 INFO @ Tue, 16 Jun 2020 10:00:12: 6000000 INFO @ Tue, 16 Jun 2020 10:00:15: 2000000 INFO @ Tue, 16 Jun 2020 10:00:19: 7000000 INFO @ Tue, 16 Jun 2020 10:00:19: 11000000 INFO @ Tue, 16 Jun 2020 10:00:22: 3000000 INFO @ Tue, 16 Jun 2020 10:00:25: 8000000 INFO @ Tue, 16 Jun 2020 10:00:26: 12000000 INFO @ Tue, 16 Jun 2020 10:00:29: 4000000 INFO @ Tue, 16 Jun 2020 10:00:32: 9000000 INFO @ Tue, 16 Jun 2020 10:00:33: 13000000 INFO @ Tue, 16 Jun 2020 10:00:36: 5000000 INFO @ Tue, 16 Jun 2020 10:00:39: 10000000 INFO @ Tue, 16 Jun 2020 10:00:40: 14000000 INFO @ Tue, 16 Jun 2020 10:00:42: 6000000 INFO @ Tue, 16 Jun 2020 10:00:45: 11000000 INFO @ Tue, 16 Jun 2020 10:00:47: 15000000 INFO @ Tue, 16 Jun 2020 10:00:49: 7000000 INFO @ Tue, 16 Jun 2020 10:00:52: 12000000 INFO @ Tue, 16 Jun 2020 10:00:54: 16000000 INFO @ Tue, 16 Jun 2020 10:00:56: 8000000 INFO @ Tue, 16 Jun 2020 10:00:59: 13000000 INFO @ Tue, 16 Jun 2020 10:01:01: 17000000 INFO @ Tue, 16 Jun 2020 10:01:02: 9000000 INFO @ Tue, 16 Jun 2020 10:01:05: 14000000 INFO @ Tue, 16 Jun 2020 10:01:08: 18000000 INFO @ Tue, 16 Jun 2020 10:01:09: 10000000 INFO @ Tue, 16 Jun 2020 10:01:12: 15000000 INFO @ Tue, 16 Jun 2020 10:01:15: 19000000 INFO @ Tue, 16 Jun 2020 10:01:15: 11000000 INFO @ Tue, 16 Jun 2020 10:01:18: 16000000 INFO @ Tue, 16 Jun 2020 10:01:22: 12000000 INFO @ Tue, 16 Jun 2020 10:01:22: 20000000 INFO @ Tue, 16 Jun 2020 10:01:25: 17000000 INFO @ Tue, 16 Jun 2020 10:01:29: 13000000 INFO @ Tue, 16 Jun 2020 10:01:29: 21000000 INFO @ Tue, 16 Jun 2020 10:01:32: 18000000 INFO @ Tue, 16 Jun 2020 10:01:35: 14000000 INFO @ Tue, 16 Jun 2020 10:01:36: 22000000 INFO @ Tue, 16 Jun 2020 10:01:38: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:01:42: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:01:42: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:01:42: #1 total tags in treatment: 22718433 INFO @ Tue, 16 Jun 2020 10:01:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:42: #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 10:01:42: #1 tags after filtering in treatment: 22718433 INFO @ Tue, 16 Jun 2020 10:01:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:42: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:42: 15000000 INFO @ Tue, 16 Jun 2020 10:01:43: #2 number of paired peaks: 785 WARNING @ Tue, 16 Jun 2020 10:01:43: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:43: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:44: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:44: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:44: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:44: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 10:01:44: #2 alternative fragment length(s) may be 3,190 bps INFO @ Tue, 16 Jun 2020 10:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.05_model.r INFO @ Tue, 16 Jun 2020 10:01:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:45: 20000000 INFO @ Tue, 16 Jun 2020 10:01:49: 16000000 INFO @ Tue, 16 Jun 2020 10:01:51: 21000000 INFO @ Tue, 16 Jun 2020 10:01:55: 17000000 INFO @ Tue, 16 Jun 2020 10:01:58: 22000000 INFO @ Tue, 16 Jun 2020 10:02:02: 18000000 INFO @ Tue, 16 Jun 2020 10:02:02: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:02:02: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:02:02: #1 total tags in treatment: 22718433 INFO @ Tue, 16 Jun 2020 10:02:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:02: #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 10:02:03: #1 tags after filtering in treatment: 22718433 INFO @ Tue, 16 Jun 2020 10:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:03: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:04: #2 number of paired peaks: 785 WARNING @ Tue, 16 Jun 2020 10:02:04: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:04: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:04: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:04: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:04: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:04: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 10:02:04: #2 alternative fragment length(s) may be 3,190 bps INFO @ Tue, 16 Jun 2020 10:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.10_model.r INFO @ Tue, 16 Jun 2020 10:02:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:08: 19000000 INFO @ Tue, 16 Jun 2020 10:02:14: 20000000 INFO @ Tue, 16 Jun 2020 10:02:20: 21000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:02:26: 22000000 INFO @ Tue, 16 Jun 2020 10:02:30: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:02:30: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:02:30: #1 total tags in treatment: 22718433 INFO @ Tue, 16 Jun 2020 10:02:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:30: #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 10:02:31: #1 tags after filtering in treatment: 22718433 INFO @ Tue, 16 Jun 2020 10:02:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:31: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:32: #2 number of paired peaks: 785 WARNING @ Tue, 16 Jun 2020 10:02:32: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:32: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:33: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:33: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:33: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:33: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 10:02:33: #2 alternative fragment length(s) may be 3,190 bps INFO @ Tue, 16 Jun 2020 10:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.20_model.r INFO @ Tue, 16 Jun 2020 10:02:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.05_summits.bed INFO @ Tue, 16 Jun 2020 10:03:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7616 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.10_summits.bed INFO @ Tue, 16 Jun 2020 10:03:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4961 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:03:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985670/SRX5985670.20_summits.bed INFO @ Tue, 16 Jun 2020 10:03:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2507 records, 4 fields): 4 millis CompletedMACS2peakCalling