Job ID = 6366852 SRX = SRX2350751 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:53 prefetch.2.10.7: 1) Downloading 'SRR5024060'... 2020-06-15T22:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:02 prefetch.2.10.7: 'SRR5024060' is valid 2020-06-15T23:01:02 prefetch.2.10.7: 1) 'SRR5024060' was downloaded successfully Read 10961380 spots for SRR5024060/SRR5024060.sra Written 10961380 spots for SRR5024060/SRR5024060.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: 00:02:18 10961380 reads; of these: 10961380 (100.00%) were unpaired; of these: 123848 (1.13%) aligned 0 times 9526932 (86.91%) aligned exactly 1 time 1310600 (11.96%) aligned >1 times 98.87% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 1627624 / 10837532 = 0.1502 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 08:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.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 08:06:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:45: 1000000 INFO @ Tue, 16 Jun 2020 08:06:52: 2000000 INFO @ Tue, 16 Jun 2020 08:06:59: 3000000 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 08:07:07: 4000000 INFO @ Tue, 16 Jun 2020 08:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.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 08:07:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:14: 5000000 INFO @ Tue, 16 Jun 2020 08:07:16: 1000000 INFO @ Tue, 16 Jun 2020 08:07:22: 6000000 INFO @ Tue, 16 Jun 2020 08:07:24: 2000000 INFO @ Tue, 16 Jun 2020 08:07:30: 7000000 INFO @ Tue, 16 Jun 2020 08:07:32: 3000000 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 08:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.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 08:07:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:38: 8000000 INFO @ Tue, 16 Jun 2020 08:07:40: 4000000 INFO @ Tue, 16 Jun 2020 08:07:45: 1000000 INFO @ Tue, 16 Jun 2020 08:07:47: 9000000 INFO @ Tue, 16 Jun 2020 08:07:48: 5000000 INFO @ Tue, 16 Jun 2020 08:07:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:48: #1 total tags in treatment: 9209908 INFO @ Tue, 16 Jun 2020 08:07:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:48: #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 08:07:48: #1 tags after filtering in treatment: 9209908 INFO @ Tue, 16 Jun 2020 08:07:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:49: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 08:07:49: 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 08:07:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:49: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 08:07:49: #2 alternative fragment length(s) may be 3,56,128,531 bps INFO @ Tue, 16 Jun 2020 08:07:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.05_model.r WARNING @ Tue, 16 Jun 2020 08:07:49: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:49: #2 You may need to consider one of the other alternative d(s): 3,56,128,531 WARNING @ Tue, 16 Jun 2020 08:07:49: #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 08:07:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:52: 2000000 INFO @ Tue, 16 Jun 2020 08:07:56: 6000000 INFO @ Tue, 16 Jun 2020 08:07:59: 3000000 INFO @ Tue, 16 Jun 2020 08:08:04: 7000000 INFO @ Tue, 16 Jun 2020 08:08:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:06: 4000000 INFO @ Tue, 16 Jun 2020 08:08:12: 8000000 INFO @ Tue, 16 Jun 2020 08:08:14: 5000000 INFO @ Tue, 16 Jun 2020 08:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (897 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:20: 9000000 INFO @ Tue, 16 Jun 2020 08:08:21: 6000000 INFO @ Tue, 16 Jun 2020 08:08:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:21: #1 total tags in treatment: 9209908 INFO @ Tue, 16 Jun 2020 08:08:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:21: #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 08:08:22: #1 tags after filtering in treatment: 9209908 INFO @ Tue, 16 Jun 2020 08:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:22: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 08:08:22: 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 08:08:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:22: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 08:08:22: #2 alternative fragment length(s) may be 3,56,128,531 bps INFO @ Tue, 16 Jun 2020 08:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.10_model.r WARNING @ Tue, 16 Jun 2020 08:08:22: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:22: #2 You may need to consider one of the other alternative d(s): 3,56,128,531 WARNING @ Tue, 16 Jun 2020 08:08:22: #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 08:08:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:27: 7000000 INFO @ Tue, 16 Jun 2020 08:08:34: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:40: 9000000 INFO @ Tue, 16 Jun 2020 08:08:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:41: #1 total tags in treatment: 9209908 INFO @ Tue, 16 Jun 2020 08:08:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:41: #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 08:08:41: #1 tags after filtering in treatment: 9209908 INFO @ Tue, 16 Jun 2020 08:08:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:42: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 08:08:42: 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 08:08:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:42: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 08:08:42: #2 alternative fragment length(s) may be 3,56,128,531 bps INFO @ Tue, 16 Jun 2020 08:08:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.20_model.r WARNING @ Tue, 16 Jun 2020 08:08:42: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:42: #2 You may need to consider one of the other alternative d(s): 3,56,128,531 WARNING @ Tue, 16 Jun 2020 08:08:42: #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 08:08:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350751/SRX2350751.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 1 millis CompletedMACS2peakCalling