Job ID = 6367583 SRX = SRX331340 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:36:30 prefetch.2.10.7: 1) Downloading 'SRR1030715'... 2020-06-15T23:36:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:29 prefetch.2.10.7: 1) 'SRR1030715' was downloaded successfully Read 22299748 spots for SRR1030715/SRR1030715.sra Written 22299748 spots for SRR1030715/SRR1030715.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: 00:05:00 22299748 reads; of these: 22299748 (100.00%) were unpaired; of these: 904814 (4.06%) aligned 0 times 18192686 (81.58%) aligned exactly 1 time 3202248 (14.36%) aligned >1 times 95.94% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 4862213 / 21394934 = 0.2273 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 08:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.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 08:53:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:55: 1000000 INFO @ Tue, 16 Jun 2020 08:54:00: 2000000 INFO @ Tue, 16 Jun 2020 08:54:06: 3000000 INFO @ Tue, 16 Jun 2020 08:54:11: 4000000 INFO @ Tue, 16 Jun 2020 08:54:16: 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 08:54:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.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 08:54:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:22: 6000000 INFO @ Tue, 16 Jun 2020 08:54:25: 1000000 INFO @ Tue, 16 Jun 2020 08:54:28: 7000000 INFO @ Tue, 16 Jun 2020 08:54:30: 2000000 INFO @ Tue, 16 Jun 2020 08:54:33: 8000000 INFO @ Tue, 16 Jun 2020 08:54:36: 3000000 INFO @ Tue, 16 Jun 2020 08:54:39: 9000000 INFO @ Tue, 16 Jun 2020 08:54:41: 4000000 INFO @ Tue, 16 Jun 2020 08:54:44: 10000000 INFO @ Tue, 16 Jun 2020 08:54:47: 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 08:54:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.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 08:54:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:50: 11000000 INFO @ Tue, 16 Jun 2020 08:54:52: 6000000 INFO @ Tue, 16 Jun 2020 08:54:55: 1000000 INFO @ Tue, 16 Jun 2020 08:54:56: 12000000 INFO @ Tue, 16 Jun 2020 08:54:58: 7000000 INFO @ Tue, 16 Jun 2020 08:55:01: 2000000 INFO @ Tue, 16 Jun 2020 08:55:01: 13000000 INFO @ Tue, 16 Jun 2020 08:55:03: 8000000 INFO @ Tue, 16 Jun 2020 08:55:06: 3000000 INFO @ Tue, 16 Jun 2020 08:55:07: 14000000 INFO @ Tue, 16 Jun 2020 08:55:08: 9000000 INFO @ Tue, 16 Jun 2020 08:55:12: 4000000 INFO @ Tue, 16 Jun 2020 08:55:13: 15000000 INFO @ Tue, 16 Jun 2020 08:55:14: 10000000 INFO @ Tue, 16 Jun 2020 08:55:17: 5000000 INFO @ Tue, 16 Jun 2020 08:55:18: 16000000 INFO @ Tue, 16 Jun 2020 08:55:19: 11000000 INFO @ Tue, 16 Jun 2020 08:55:22: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:22: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:22: #1 total tags in treatment: 16532721 INFO @ Tue, 16 Jun 2020 08:55:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:22: #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 08:55:22: #1 tags after filtering in treatment: 16532721 INFO @ Tue, 16 Jun 2020 08:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:23: 6000000 INFO @ Tue, 16 Jun 2020 08:55:23: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 08:55:23: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:23: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:55:23: #2 alternative fragment length(s) may be 3,130,148 bps INFO @ Tue, 16 Jun 2020 08:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.05_model.r INFO @ Tue, 16 Jun 2020 08:55:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:25: 12000000 INFO @ Tue, 16 Jun 2020 08:55:28: 7000000 INFO @ Tue, 16 Jun 2020 08:55:30: 13000000 INFO @ Tue, 16 Jun 2020 08:55:33: 8000000 INFO @ Tue, 16 Jun 2020 08:55:36: 14000000 INFO @ Tue, 16 Jun 2020 08:55:39: 9000000 INFO @ Tue, 16 Jun 2020 08:55:41: 15000000 INFO @ Tue, 16 Jun 2020 08:55:44: 10000000 INFO @ Tue, 16 Jun 2020 08:55:46: 16000000 INFO @ Tue, 16 Jun 2020 08:55:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:50: #1 total tags in treatment: 16532721 INFO @ Tue, 16 Jun 2020 08:55:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:50: #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 08:55:50: 11000000 INFO @ Tue, 16 Jun 2020 08:55:50: #1 tags after filtering in treatment: 16532721 INFO @ Tue, 16 Jun 2020 08:55:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:51: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 08:55:51: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:51: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:55:51: #2 alternative fragment length(s) may be 3,130,148 bps INFO @ Tue, 16 Jun 2020 08:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.10_model.r INFO @ Tue, 16 Jun 2020 08:55:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:55: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:00: 13000000 INFO @ Tue, 16 Jun 2020 08:56:06: 14000000 INFO @ Tue, 16 Jun 2020 08:56:11: 15000000 INFO @ Tue, 16 Jun 2020 08:56:16: 16000000 INFO @ Tue, 16 Jun 2020 08:56:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:19: #1 total tags in treatment: 16532721 INFO @ Tue, 16 Jun 2020 08:56:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:19: #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 08:56:20: #1 tags after filtering in treatment: 16532721 INFO @ Tue, 16 Jun 2020 08:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:21: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10215 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:21: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 08:56:21: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:21: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:56:21: #2 alternative fragment length(s) may be 3,130,148 bps INFO @ Tue, 16 Jun 2020 08:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.20_model.r INFO @ Tue, 16 Jun 2020 08:56:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.10_summits.bed INFO @ Tue, 16 Jun 2020 08:56:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4033 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331340/SRX331340.20_summits.bed INFO @ Tue, 16 Jun 2020 08:57:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 2 millis CompletedMACS2peakCalling