Job ID = 6368908 SRX = SRX6720173 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:37:49 prefetch.2.10.7: 1) Downloading 'SRR9972857'... 2020-06-16T00:37:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:23 prefetch.2.10.7: 'SRR9972857' is valid 2020-06-16T00:40:23 prefetch.2.10.7: 1) 'SRR9972857' was downloaded successfully Read 10465322 spots for SRR9972857/SRR9972857.sra Written 10465322 spots for SRR9972857/SRR9972857.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: 00:02:13 10465322 reads; of these: 10465322 (100.00%) were unpaired; of these: 558532 (5.34%) aligned 0 times 8514784 (81.36%) aligned exactly 1 time 1392006 (13.30%) aligned >1 times 94.66% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 1480163 / 9906790 = 0.1494 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 09:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.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 09:46:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:14: 1000000 INFO @ Tue, 16 Jun 2020 09:46:19: 2000000 INFO @ Tue, 16 Jun 2020 09:46:24: 3000000 INFO @ Tue, 16 Jun 2020 09:46:30: 4000000 INFO @ Tue, 16 Jun 2020 09:46:35: 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 09:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.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 09:46:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:41: 6000000 INFO @ Tue, 16 Jun 2020 09:46:43: 1000000 INFO @ Tue, 16 Jun 2020 09:46:46: 7000000 INFO @ Tue, 16 Jun 2020 09:46:49: 2000000 INFO @ Tue, 16 Jun 2020 09:46:52: 8000000 INFO @ Tue, 16 Jun 2020 09:46:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:54: #1 total tags in treatment: 8426627 INFO @ Tue, 16 Jun 2020 09:46:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:54: #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 09:46:55: #1 tags after filtering in treatment: 8426627 INFO @ Tue, 16 Jun 2020 09:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:55: 3000000 INFO @ Tue, 16 Jun 2020 09:46:55: #2 number of paired peaks: 728 WARNING @ Tue, 16 Jun 2020 09:46:55: Fewer paired peaks (728) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 728 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:55: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:46:55: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 09:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.05_model.r INFO @ Tue, 16 Jun 2020 09:46:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:00: 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 09:47:06: 5000000 INFO @ Tue, 16 Jun 2020 09:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.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 09:47:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:11: 6000000 INFO @ Tue, 16 Jun 2020 09:47:13: 1000000 INFO @ Tue, 16 Jun 2020 09:47:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:17: 7000000 INFO @ Tue, 16 Jun 2020 09:47:19: 2000000 INFO @ Tue, 16 Jun 2020 09:47:22: 8000000 INFO @ Tue, 16 Jun 2020 09:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3673 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:25: 3000000 INFO @ Tue, 16 Jun 2020 09:47:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:25: #1 total tags in treatment: 8426627 INFO @ Tue, 16 Jun 2020 09:47:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:25: #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 09:47:25: #1 tags after filtering in treatment: 8426627 INFO @ Tue, 16 Jun 2020 09:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:26: #2 number of paired peaks: 728 WARNING @ Tue, 16 Jun 2020 09:47:26: Fewer paired peaks (728) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 728 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:26: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:47:26: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 09:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.10_model.r INFO @ Tue, 16 Jun 2020 09:47:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:30: 4000000 INFO @ Tue, 16 Jun 2020 09:47:36: 5000000 INFO @ Tue, 16 Jun 2020 09:47:42: 6000000 INFO @ Tue, 16 Jun 2020 09:47:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:47: 7000000 INFO @ Tue, 16 Jun 2020 09:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1759 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:53: 8000000 INFO @ Tue, 16 Jun 2020 09:47:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:56: #1 total tags in treatment: 8426627 INFO @ Tue, 16 Jun 2020 09:47:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:56: #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 09:47:56: #1 tags after filtering in treatment: 8426627 INFO @ Tue, 16 Jun 2020 09:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:56: #2 number of paired peaks: 728 WARNING @ Tue, 16 Jun 2020 09:47:56: Fewer paired peaks (728) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 728 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:57: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:47:57: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 09:47:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.20_model.r INFO @ Tue, 16 Jun 2020 09:47:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:48:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720173/SRX6720173.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (612 records, 4 fields): 2 millis CompletedMACS2peakCalling