Job ID = 6507988 SRX = SRX657410 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:17:49 prefetch.2.10.7: 1) Downloading 'SRR1520419'... 2020-06-26T13:17:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:18:49 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:18:49 prefetch.2.10.7: 'SRR1520419' is valid 2020-06-26T13:18:49 prefetch.2.10.7: 1) 'SRR1520419' was downloaded successfully Read 8712390 spots for SRR1520419/SRR1520419.sra Written 8712390 spots for SRR1520419/SRR1520419.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: 00:00:01 Multiseed full-index search: 00:01:32 8712390 reads; of these: 8712390 (100.00%) were unpaired; of these: 2437211 (27.97%) aligned 0 times 5097000 (58.50%) aligned exactly 1 time 1178179 (13.52%) aligned >1 times 72.03% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 543582 / 6275179 = 0.0866 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 @ Fri, 26 Jun 2020 22:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.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 @ Fri, 26 Jun 2020 22:22:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:22:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:22:54: 1000000 INFO @ Fri, 26 Jun 2020 22:23:00: 2000000 INFO @ Fri, 26 Jun 2020 22:23:06: 3000000 INFO @ Fri, 26 Jun 2020 22:23:12: 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 @ Fri, 26 Jun 2020 22:23:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.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 @ Fri, 26 Jun 2020 22:23:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:23:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:23:18: 5000000 INFO @ Fri, 26 Jun 2020 22:23:23: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 22:23:23: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 22:23:23: #1 total tags in treatment: 5731597 INFO @ Fri, 26 Jun 2020 22:23:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:23:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:23:23: #1 tags after filtering in treatment: 5731597 INFO @ Fri, 26 Jun 2020 22:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:23:23: #1 finished! INFO @ Fri, 26 Jun 2020 22:23:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:23:24: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 22:23:24: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 22:23:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:23:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:23:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:23:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:23:24: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 22:23:24: #2 alternative fragment length(s) may be 4,47,542,565 bps INFO @ Fri, 26 Jun 2020 22:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.05_model.r WARNING @ Fri, 26 Jun 2020 22:23:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:23:24: #2 You may need to consider one of the other alternative d(s): 4,47,542,565 WARNING @ Fri, 26 Jun 2020 22:23:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:23:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:23:24: 1000000 INFO @ Fri, 26 Jun 2020 22:23:29: 2000000 INFO @ Fri, 26 Jun 2020 22:23:35: 3000000 INFO @ Fri, 26 Jun 2020 22:23:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:23:40: 4000000 INFO @ Fri, 26 Jun 2020 22:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.05_summits.bed INFO @ Fri, 26 Jun 2020 22:23:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (573 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Fri, 26 Jun 2020 22:23:46: 5000000 INFO @ Fri, 26 Jun 2020 22:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.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 @ Fri, 26 Jun 2020 22:23:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:23:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:23:50: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 22:23:50: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 22:23:50: #1 total tags in treatment: 5731597 INFO @ Fri, 26 Jun 2020 22:23:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:23:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:23:50: #1 tags after filtering in treatment: 5731597 INFO @ Fri, 26 Jun 2020 22:23:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:23:50: #1 finished! INFO @ Fri, 26 Jun 2020 22:23:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:23:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:23:51: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 22:23:51: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 22:23:51: start model_add_line... INFO @ Fri, 26 Jun 2020 22:23:51: start X-correlation... INFO @ Fri, 26 Jun 2020 22:23:51: end of X-cor INFO @ Fri, 26 Jun 2020 22:23:51: #2 finished! INFO @ Fri, 26 Jun 2020 22:23:51: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 22:23:51: #2 alternative fragment length(s) may be 4,47,542,565 bps INFO @ Fri, 26 Jun 2020 22:23:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.10_model.r WARNING @ Fri, 26 Jun 2020 22:23:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:23:51: #2 You may need to consider one of the other alternative d(s): 4,47,542,565 WARNING @ Fri, 26 Jun 2020 22:23:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:23:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:23:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:23:53: 1000000 INFO @ Fri, 26 Jun 2020 22:23:59: 2000000 INFO @ Fri, 26 Jun 2020 22:24:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:24:05: 3000000 INFO @ Fri, 26 Jun 2020 22:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.10_summits.bed INFO @ Fri, 26 Jun 2020 22:24:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:24:10: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:24:16: 5000000 INFO @ Fri, 26 Jun 2020 22:24:20: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 22:24:20: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 22:24:20: #1 total tags in treatment: 5731597 INFO @ Fri, 26 Jun 2020 22:24:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:24:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:24:20: #1 tags after filtering in treatment: 5731597 INFO @ Fri, 26 Jun 2020 22:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:24:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:24:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:24:21: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 22:24:21: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 22:24:21: start model_add_line... INFO @ Fri, 26 Jun 2020 22:24:21: start X-correlation... INFO @ Fri, 26 Jun 2020 22:24:21: end of X-cor INFO @ Fri, 26 Jun 2020 22:24:21: #2 finished! INFO @ Fri, 26 Jun 2020 22:24:21: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 22:24:21: #2 alternative fragment length(s) may be 4,47,542,565 bps INFO @ Fri, 26 Jun 2020 22:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.20_model.r WARNING @ Fri, 26 Jun 2020 22:24:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:24:21: #2 You may need to consider one of the other alternative d(s): 4,47,542,565 WARNING @ Fri, 26 Jun 2020 22:24:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:24:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:24:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:24:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657410/SRX657410.20_summits.bed INFO @ Fri, 26 Jun 2020 22:24:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling