Job ID = 6367644 SRX = SRX373266 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:49:48 prefetch.2.10.7: 1) Downloading 'SRR1024184'... 2020-06-15T23:49:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:41 prefetch.2.10.7: 1) 'SRR1024184' was downloaded successfully Read 18184450 spots for SRR1024184/SRR1024184.sra Written 18184450 spots for SRR1024184/SRR1024184.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: 00:04:01 18184450 reads; of these: 18184450 (100.00%) were unpaired; of these: 1329375 (7.31%) aligned 0 times 13803351 (75.91%) aligned exactly 1 time 3051724 (16.78%) aligned >1 times 92.69% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 5274856 / 16855075 = 0.3130 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 09:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.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 09:00:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:48: 1000000 INFO @ Tue, 16 Jun 2020 09:00:55: 2000000 INFO @ Tue, 16 Jun 2020 09:01:02: 3000000 INFO @ Tue, 16 Jun 2020 09:01:09: 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 09:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.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 09:01:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:16: 5000000 INFO @ Tue, 16 Jun 2020 09:01:18: 1000000 INFO @ Tue, 16 Jun 2020 09:01:24: 6000000 INFO @ Tue, 16 Jun 2020 09:01:25: 2000000 INFO @ Tue, 16 Jun 2020 09:01:31: 7000000 INFO @ Tue, 16 Jun 2020 09:01:32: 3000000 INFO @ Tue, 16 Jun 2020 09:01:39: 8000000 INFO @ Tue, 16 Jun 2020 09:01:39: 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 09:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.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 09:01:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:46: 5000000 INFO @ Tue, 16 Jun 2020 09:01:47: 9000000 INFO @ Tue, 16 Jun 2020 09:01:50: 1000000 INFO @ Tue, 16 Jun 2020 09:01:53: 6000000 INFO @ Tue, 16 Jun 2020 09:01:54: 10000000 INFO @ Tue, 16 Jun 2020 09:01:58: 2000000 INFO @ Tue, 16 Jun 2020 09:02:00: 7000000 INFO @ Tue, 16 Jun 2020 09:02:02: 11000000 INFO @ Tue, 16 Jun 2020 09:02:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:07: #1 total tags in treatment: 11580219 INFO @ Tue, 16 Jun 2020 09:02:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:07: #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 09:02:07: #1 tags after filtering in treatment: 11580219 INFO @ Tue, 16 Jun 2020 09:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:07: 3000000 INFO @ Tue, 16 Jun 2020 09:02:08: 8000000 INFO @ Tue, 16 Jun 2020 09:02:08: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 09:02:08: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:08: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:02:08: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:08: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:02:08: #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 09:02:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:14: 9000000 INFO @ Tue, 16 Jun 2020 09:02:16: 4000000 INFO @ Tue, 16 Jun 2020 09:02:21: 10000000 INFO @ Tue, 16 Jun 2020 09:02:24: 5000000 INFO @ Tue, 16 Jun 2020 09:02:29: 11000000 INFO @ Tue, 16 Jun 2020 09:02:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:32: 6000000 INFO @ Tue, 16 Jun 2020 09:02:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:33: #1 total tags in treatment: 11580219 INFO @ Tue, 16 Jun 2020 09:02:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:33: #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 09:02:33: #1 tags after filtering in treatment: 11580219 INFO @ Tue, 16 Jun 2020 09:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:34: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 09:02:34: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:34: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:02:34: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.10_model.r WARNING @ Tue, 16 Jun 2020 09:02:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:34: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:02:34: #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 09:02:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:40: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:47: 8000000 INFO @ Tue, 16 Jun 2020 09:02:54: 9000000 INFO @ Tue, 16 Jun 2020 09:02:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:02: 10000000 INFO @ Tue, 16 Jun 2020 09:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:06: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:09: 11000000 INFO @ Tue, 16 Jun 2020 09:03:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:14: #1 total tags in treatment: 11580219 INFO @ Tue, 16 Jun 2020 09:03:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:14: #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 09:03:14: #1 tags after filtering in treatment: 11580219 INFO @ Tue, 16 Jun 2020 09:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:15: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 09:03:15: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:15: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:03:15: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:03:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:15: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:03:15: #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 09:03:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373266/SRX373266.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 1 millis CompletedMACS2peakCalling