Job ID = 6368818 SRX = SRX5985672 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:34 prefetch.2.10.7: 1) Downloading 'SRR9214977'... 2020-06-16T00:28:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:00 prefetch.2.10.7: 1) 'SRR9214977' was downloaded successfully Read 21089109 spots for SRR9214977/SRR9214977.sra Written 21089109 spots for SRR9214977/SRR9214977.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: 00:05:03 21089109 reads; of these: 21089109 (100.00%) were unpaired; of these: 6868889 (32.57%) aligned 0 times 12529181 (59.41%) aligned exactly 1 time 1691039 (8.02%) aligned >1 times 67.43% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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 8 files... [bam_rmdupse_core] 4594916 / 14220220 = 0.3231 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 09:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.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 09:43:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:05: 1000000 INFO @ Tue, 16 Jun 2020 09:44:11: 2000000 INFO @ Tue, 16 Jun 2020 09:44:18: 3000000 INFO @ Tue, 16 Jun 2020 09:44:24: 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 09:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.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 09:44:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:31: 5000000 INFO @ Tue, 16 Jun 2020 09:44:35: 1000000 INFO @ Tue, 16 Jun 2020 09:44:37: 6000000 INFO @ Tue, 16 Jun 2020 09:44:42: 2000000 INFO @ Tue, 16 Jun 2020 09:44:44: 7000000 INFO @ Tue, 16 Jun 2020 09:44:49: 3000000 INFO @ Tue, 16 Jun 2020 09:44:51: 8000000 INFO @ Tue, 16 Jun 2020 09:44:56: 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 09:44:58: 9000000 INFO @ Tue, 16 Jun 2020 09:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.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 09:44:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:45:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:45:03: #1 total tags in treatment: 9625304 INFO @ Tue, 16 Jun 2020 09:45:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:03: #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 09:45:03: #1 tags after filtering in treatment: 9625304 INFO @ Tue, 16 Jun 2020 09:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:03: 5000000 INFO @ Tue, 16 Jun 2020 09:45:04: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 09:45:04: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:04: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:45:04: #2 alternative fragment length(s) may be 4,157 bps INFO @ Tue, 16 Jun 2020 09:45:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.05_model.r INFO @ Tue, 16 Jun 2020 09:45:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:07: 1000000 INFO @ Tue, 16 Jun 2020 09:45:10: 6000000 INFO @ Tue, 16 Jun 2020 09:45:15: 2000000 INFO @ Tue, 16 Jun 2020 09:45:18: 7000000 INFO @ Tue, 16 Jun 2020 09:45:24: 3000000 INFO @ Tue, 16 Jun 2020 09:45:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:26: 8000000 INFO @ Tue, 16 Jun 2020 09:45:33: 4000000 INFO @ Tue, 16 Jun 2020 09:45:33: 9000000 INFO @ Tue, 16 Jun 2020 09:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6458 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:38: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:45:38: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:45:38: #1 total tags in treatment: 9625304 INFO @ Tue, 16 Jun 2020 09:45:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:38: #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 09:45:38: #1 tags after filtering in treatment: 9625304 INFO @ Tue, 16 Jun 2020 09:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:39: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 09:45:39: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:39: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:45:39: #2 alternative fragment length(s) may be 4,157 bps INFO @ Tue, 16 Jun 2020 09:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.10_model.r INFO @ Tue, 16 Jun 2020 09:45:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:41: 5000000 INFO @ Tue, 16 Jun 2020 09:45:49: 6000000 INFO @ Tue, 16 Jun 2020 09:45:57: 7000000 INFO @ Tue, 16 Jun 2020 09:45:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:05: 8000000 INFO @ Tue, 16 Jun 2020 09:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2273 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:13: 9000000 INFO @ Tue, 16 Jun 2020 09:46:18: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:46:18: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:46:18: #1 total tags in treatment: 9625304 INFO @ Tue, 16 Jun 2020 09:46:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:18: #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 09:46:18: #1 tags after filtering in treatment: 9625304 INFO @ Tue, 16 Jun 2020 09:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:18: #2 number of paired peaks: 709 WARNING @ Tue, 16 Jun 2020 09:46:18: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:18: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:46:18: #2 alternative fragment length(s) may be 4,157 bps INFO @ Tue, 16 Jun 2020 09:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.20_model.r INFO @ Tue, 16 Jun 2020 09:46:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985672/SRX5985672.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling