Job ID = 6368035 SRX = SRX466498 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:43:29 prefetch.2.10.7: 1) Downloading 'SRR1163564'... 2020-06-15T23:43:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:04 prefetch.2.10.7: 1) 'SRR1163564' was downloaded successfully Read 34080196 spots for SRR1163564/SRR1163564.sra Written 34080196 spots for SRR1163564/SRR1163564.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: 00:09:09 34080196 reads; of these: 34080196 (100.00%) were unpaired; of these: 1431834 (4.20%) aligned 0 times 20950047 (61.47%) aligned exactly 1 time 11698315 (34.33%) aligned >1 times 95.80% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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_sort_core] merging from 16 files... [bam_rmdupse_core] 13710654 / 32648362 = 0.4199 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 09:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.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 09:06:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:47: 1000000 INFO @ Tue, 16 Jun 2020 09:06:54: 2000000 INFO @ Tue, 16 Jun 2020 09:07:01: 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 09:07:09: 4000000 INFO @ Tue, 16 Jun 2020 09:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.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 09:07:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:16: 5000000 INFO @ Tue, 16 Jun 2020 09:07:17: 1000000 INFO @ Tue, 16 Jun 2020 09:07:24: 6000000 INFO @ Tue, 16 Jun 2020 09:07:25: 2000000 INFO @ Tue, 16 Jun 2020 09:07:32: 3000000 INFO @ Tue, 16 Jun 2020 09:07:33: 7000000 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 09:07:39: 4000000 INFO @ Tue, 16 Jun 2020 09:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.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 09:07:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:41: 8000000 INFO @ Tue, 16 Jun 2020 09:07:47: 5000000 INFO @ Tue, 16 Jun 2020 09:07:48: 1000000 INFO @ Tue, 16 Jun 2020 09:07:49: 9000000 INFO @ Tue, 16 Jun 2020 09:07:54: 6000000 INFO @ Tue, 16 Jun 2020 09:07:56: 2000000 INFO @ Tue, 16 Jun 2020 09:07:57: 10000000 INFO @ Tue, 16 Jun 2020 09:08:02: 7000000 INFO @ Tue, 16 Jun 2020 09:08:04: 3000000 INFO @ Tue, 16 Jun 2020 09:08:05: 11000000 INFO @ Tue, 16 Jun 2020 09:08:09: 8000000 INFO @ Tue, 16 Jun 2020 09:08:12: 4000000 INFO @ Tue, 16 Jun 2020 09:08:13: 12000000 INFO @ Tue, 16 Jun 2020 09:08:17: 9000000 INFO @ Tue, 16 Jun 2020 09:08:20: 5000000 INFO @ Tue, 16 Jun 2020 09:08:21: 13000000 INFO @ Tue, 16 Jun 2020 09:08:24: 10000000 INFO @ Tue, 16 Jun 2020 09:08:28: 6000000 INFO @ Tue, 16 Jun 2020 09:08:29: 14000000 INFO @ Tue, 16 Jun 2020 09:08:32: 11000000 INFO @ Tue, 16 Jun 2020 09:08:37: 7000000 INFO @ Tue, 16 Jun 2020 09:08:38: 15000000 INFO @ Tue, 16 Jun 2020 09:08:40: 12000000 INFO @ Tue, 16 Jun 2020 09:08:46: 8000000 INFO @ Tue, 16 Jun 2020 09:08:46: 16000000 INFO @ Tue, 16 Jun 2020 09:08:47: 13000000 INFO @ Tue, 16 Jun 2020 09:08:54: 17000000 INFO @ Tue, 16 Jun 2020 09:08:54: 9000000 INFO @ Tue, 16 Jun 2020 09:08:54: 14000000 INFO @ Tue, 16 Jun 2020 09:09:02: 15000000 INFO @ Tue, 16 Jun 2020 09:09:03: 18000000 INFO @ Tue, 16 Jun 2020 09:09:03: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:09:09: 16000000 INFO @ Tue, 16 Jun 2020 09:09:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:09:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:09:10: #1 total tags in treatment: 18937708 INFO @ Tue, 16 Jun 2020 09:09:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:10: #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 09:09:11: #1 tags after filtering in treatment: 18937708 INFO @ Tue, 16 Jun 2020 09:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:11: 11000000 INFO @ Tue, 16 Jun 2020 09:09:12: #2 number of paired peaks: 1485 INFO @ Tue, 16 Jun 2020 09:09:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:12: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:09:12: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.05_model.r WARNING @ Tue, 16 Jun 2020 09:09:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:12: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:09:12: #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 09:09:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:17: 17000000 INFO @ Tue, 16 Jun 2020 09:09:19: 12000000 INFO @ Tue, 16 Jun 2020 09:09:24: 18000000 INFO @ Tue, 16 Jun 2020 09:09:27: 13000000 INFO @ Tue, 16 Jun 2020 09:09:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:09:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:09:31: #1 total tags in treatment: 18937708 INFO @ Tue, 16 Jun 2020 09:09:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:31: #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 09:09:31: #1 tags after filtering in treatment: 18937708 INFO @ Tue, 16 Jun 2020 09:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:33: #2 number of paired peaks: 1485 INFO @ Tue, 16 Jun 2020 09:09:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:33: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:09:33: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.10_model.r WARNING @ Tue, 16 Jun 2020 09:09:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:33: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:09:33: #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 09:09:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:34: 14000000 INFO @ Tue, 16 Jun 2020 09:09:41: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:09:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:48: 16000000 INFO @ Tue, 16 Jun 2020 09:09:56: 17000000 INFO @ Tue, 16 Jun 2020 09:10:03: 18000000 INFO @ Tue, 16 Jun 2020 09:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5833 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:09: #1 total tags in treatment: 18937708 INFO @ Tue, 16 Jun 2020 09:10:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:09: #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 09:10:10: #1 tags after filtering in treatment: 18937708 INFO @ Tue, 16 Jun 2020 09:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:11: #2 number of paired peaks: 1485 INFO @ Tue, 16 Jun 2020 09:10:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:11: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:10:11: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.20_model.r WARNING @ Tue, 16 Jun 2020 09:10:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:11: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:10:11: #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 09:10:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2442 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466498/SRX466498.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (677 records, 4 fields): 2 millis CompletedMACS2peakCalling