Job ID = 6365949 SRX = SRX043881 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:33:36 prefetch.2.10.7: 1) Downloading 'SRR107356'... 2020-06-15T22:33:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:06 prefetch.2.10.7: 'SRR107356' is valid 2020-06-15T22:34:06 prefetch.2.10.7: 1) 'SRR107356' was downloaded successfully Read 3980441 spots for SRR107356/SRR107356.sra Written 3980441 spots for SRR107356/SRR107356.sra 2020-06-15T22:34:29 prefetch.2.10.7: 1) Downloading 'SRR107357'... 2020-06-15T22:34:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:52 prefetch.2.10.7: 'SRR107357' is valid 2020-06-15T22:34:52 prefetch.2.10.7: 1) 'SRR107357' was downloaded successfully Read 4146392 spots for SRR107357/SRR107357.sra Written 4146392 spots for SRR107357/SRR107357.sra 2020-06-15T22:35:15 prefetch.2.10.7: 1) Downloading 'SRR107358'... 2020-06-15T22:35:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:35:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:35:51 prefetch.2.10.7: 'SRR107358' is valid 2020-06-15T22:35:51 prefetch.2.10.7: 1) 'SRR107358' was downloaded successfully Read 4161350 spots for SRR107358/SRR107358.sra Written 4161350 spots for SRR107358/SRR107358.sra 2020-06-15T22:36:14 prefetch.2.10.7: 1) Downloading 'SRR107359'... 2020-06-15T22:36:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:54 prefetch.2.10.7: 'SRR107359' is valid 2020-06-15T22:36:54 prefetch.2.10.7: 1) 'SRR107359' was downloaded successfully Read 4478436 spots for SRR107359/SRR107359.sra Written 4478436 spots for SRR107359/SRR107359.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: 00:01:09 16766619 reads; of these: 16766619 (100.00%) were unpaired; of these: 16030918 (95.61%) aligned 0 times 649384 (3.87%) aligned exactly 1 time 86317 (0.51%) aligned >1 times 4.39% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 19596 / 735701 = 0.0266 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 07:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.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 07:39:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:12: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:39:12: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:39:12: #1 total tags in treatment: 716105 INFO @ Tue, 16 Jun 2020 07:39:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:12: #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 07:39:12: #1 tags after filtering in treatment: 716105 INFO @ Tue, 16 Jun 2020 07:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:12: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 07:39:12: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:12: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:12: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:12: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:12: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:12: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:39:12: #2 alternative fragment length(s) may be 40,105,147,217,478,511,531 bps INFO @ Tue, 16 Jun 2020 07:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.05_model.r WARNING @ Tue, 16 Jun 2020 07:39:12: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:39:12: #2 You may need to consider one of the other alternative d(s): 40,105,147,217,478,511,531 WARNING @ Tue, 16 Jun 2020 07:39:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:39:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.05_summits.bed INFO @ Tue, 16 Jun 2020 07:39:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.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 07:39:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:42: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:39:42: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:39:42: #1 total tags in treatment: 716105 INFO @ Tue, 16 Jun 2020 07:39:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:42: #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 07:39:42: #1 tags after filtering in treatment: 716105 INFO @ Tue, 16 Jun 2020 07:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:42: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:42: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 07:39:42: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:42: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:39:42: #2 alternative fragment length(s) may be 40,105,147,217,478,511,531 bps INFO @ Tue, 16 Jun 2020 07:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.10_model.r WARNING @ Tue, 16 Jun 2020 07:39:42: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:39:42: #2 You may need to consider one of the other alternative d(s): 40,105,147,217,478,511,531 WARNING @ Tue, 16 Jun 2020 07:39:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:39:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.10_summits.bed INFO @ Tue, 16 Jun 2020 07:39:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 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 @ Tue, 16 Jun 2020 07:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.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 07:40:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:09: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:40:13: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:40:13: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:40:13: #1 total tags in treatment: 716105 INFO @ Tue, 16 Jun 2020 07:40:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:13: #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 07:40:13: #1 tags after filtering in treatment: 716105 INFO @ Tue, 16 Jun 2020 07:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:13: #2 number of paired peaks: 202 WARNING @ Tue, 16 Jun 2020 07:40:13: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:13: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:40:13: #2 alternative fragment length(s) may be 40,105,147,217,478,511,531 bps INFO @ Tue, 16 Jun 2020 07:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.20_model.r WARNING @ Tue, 16 Jun 2020 07:40:13: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:40:13: #2 You may need to consider one of the other alternative d(s): 40,105,147,217,478,511,531 WARNING @ Tue, 16 Jun 2020 07:40:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:40:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043881/SRX043881.20_summits.bed INFO @ Tue, 16 Jun 2020 07:40:16: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling