Job ID = 6367011 SRX = SRX257709 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:14 prefetch.2.10.7: 1) Downloading 'SRR800729'... 2020-06-15T23:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:29 prefetch.2.10.7: 'SRR800729' is valid 2020-06-15T23:41:29 prefetch.2.10.7: 1) 'SRR800729' was downloaded successfully Read 12861456 spots for SRR800729/SRR800729.sra Written 12861456 spots for SRR800729/SRR800729.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: 00:03:06 12861456 reads; of these: 12861456 (100.00%) were unpaired; of these: 389574 (3.03%) aligned 0 times 10387705 (80.77%) aligned exactly 1 time 2084177 (16.20%) aligned >1 times 96.97% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 875740 / 12471882 = 0.0702 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 08:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.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 08:48:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:52: 1000000 INFO @ Tue, 16 Jun 2020 08:48:58: 2000000 INFO @ Tue, 16 Jun 2020 08:49:04: 3000000 INFO @ Tue, 16 Jun 2020 08:49:10: 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 08:49:16: 5000000 INFO @ Tue, 16 Jun 2020 08:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.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 08:49:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:22: 6000000 INFO @ Tue, 16 Jun 2020 08:49:23: 1000000 INFO @ Tue, 16 Jun 2020 08:49:29: 7000000 INFO @ Tue, 16 Jun 2020 08:49:30: 2000000 INFO @ Tue, 16 Jun 2020 08:49:36: 8000000 INFO @ Tue, 16 Jun 2020 08:49:37: 3000000 INFO @ Tue, 16 Jun 2020 08:49:43: 9000000 INFO @ Tue, 16 Jun 2020 08:49:44: 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 08:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.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 08:49:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:50: 10000000 INFO @ Tue, 16 Jun 2020 08:49:51: 5000000 INFO @ Tue, 16 Jun 2020 08:49:54: 1000000 INFO @ Tue, 16 Jun 2020 08:49:57: 11000000 INFO @ Tue, 16 Jun 2020 08:49:59: 6000000 INFO @ Tue, 16 Jun 2020 08:50:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:02: #1 total tags in treatment: 11596142 INFO @ Tue, 16 Jun 2020 08:50:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:02: #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 08:50:02: #1 tags after filtering in treatment: 11596142 INFO @ Tue, 16 Jun 2020 08:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:03: #2 number of paired peaks: 309 WARNING @ Tue, 16 Jun 2020 08:50:03: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:03: 2000000 INFO @ Tue, 16 Jun 2020 08:50:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:03: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:50:03: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Tue, 16 Jun 2020 08:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:03: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:03: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Tue, 16 Jun 2020 08:50:03: #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 08:50:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:06: 7000000 INFO @ Tue, 16 Jun 2020 08:50:10: 3000000 INFO @ Tue, 16 Jun 2020 08:50:14: 8000000 INFO @ Tue, 16 Jun 2020 08:50:17: 4000000 INFO @ Tue, 16 Jun 2020 08:50:21: 9000000 INFO @ Tue, 16 Jun 2020 08:50:24: 5000000 INFO @ Tue, 16 Jun 2020 08:50:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:28: 10000000 INFO @ Tue, 16 Jun 2020 08:50:31: 6000000 INFO @ Tue, 16 Jun 2020 08:50:35: 11000000 INFO @ Tue, 16 Jun 2020 08:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (576 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:38: 7000000 INFO @ Tue, 16 Jun 2020 08:50:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:50:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:50:39: #1 total tags in treatment: 11596142 INFO @ Tue, 16 Jun 2020 08:50:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:39: #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 08:50:39: #1 tags after filtering in treatment: 11596142 INFO @ Tue, 16 Jun 2020 08:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:40: #2 number of paired peaks: 309 WARNING @ Tue, 16 Jun 2020 08:50:40: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:40: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:50:40: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Tue, 16 Jun 2020 08:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:40: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Tue, 16 Jun 2020 08:50:40: #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 08:50:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:44: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:51: 9000000 INFO @ Tue, 16 Jun 2020 08:50:57: 10000000 INFO @ Tue, 16 Jun 2020 08:51:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:03: 11000000 INFO @ Tue, 16 Jun 2020 08:51:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:51:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:51:07: #1 total tags in treatment: 11596142 INFO @ Tue, 16 Jun 2020 08:51:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:07: #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 08:51:07: #1 tags after filtering in treatment: 11596142 INFO @ Tue, 16 Jun 2020 08:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:08: #2 number of paired peaks: 309 WARNING @ Tue, 16 Jun 2020 08:51:08: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:08: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:51:08: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Tue, 16 Jun 2020 08:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:08: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Tue, 16 Jun 2020 08:51:08: #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 08:51:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257709/SRX257709.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling