Job ID = 6367999 SRX = SRX466462 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:05:16 prefetch.2.10.7: 1) Downloading 'SRR1163528'... 2020-06-16T00:05:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:08:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:08:56 prefetch.2.10.7: 1) 'SRR1163528' was downloaded successfully Read 18196513 spots for SRR1163528/SRR1163528.sra Written 18196513 spots for SRR1163528/SRR1163528.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: 00:04:14 18196513 reads; of these: 18196513 (100.00%) were unpaired; of these: 550346 (3.02%) aligned 0 times 12352371 (67.88%) aligned exactly 1 time 5293796 (29.09%) aligned >1 times 96.98% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 4809011 / 17646167 = 0.2725 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 09:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.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 09:18:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:44: 1000000 INFO @ Tue, 16 Jun 2020 09:18:50: 2000000 INFO @ Tue, 16 Jun 2020 09:18:55: 3000000 INFO @ Tue, 16 Jun 2020 09:19:00: 4000000 INFO @ Tue, 16 Jun 2020 09:19:06: 5000000 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 09:19:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.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 09:19:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:12: 6000000 INFO @ Tue, 16 Jun 2020 09:19:15: 1000000 INFO @ Tue, 16 Jun 2020 09:19:17: 7000000 INFO @ Tue, 16 Jun 2020 09:19:21: 2000000 INFO @ Tue, 16 Jun 2020 09:19:23: 8000000 INFO @ Tue, 16 Jun 2020 09:19:27: 3000000 INFO @ Tue, 16 Jun 2020 09:19:29: 9000000 INFO @ Tue, 16 Jun 2020 09:19:33: 4000000 INFO @ Tue, 16 Jun 2020 09:19:35: 10000000 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 09:19:38: 5000000 INFO @ Tue, 16 Jun 2020 09:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.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 09:19:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:41: 11000000 INFO @ Tue, 16 Jun 2020 09:19:44: 6000000 INFO @ Tue, 16 Jun 2020 09:19:45: 1000000 INFO @ Tue, 16 Jun 2020 09:19:47: 12000000 INFO @ Tue, 16 Jun 2020 09:19:51: 7000000 INFO @ Tue, 16 Jun 2020 09:19:51: 2000000 INFO @ Tue, 16 Jun 2020 09:19:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:19:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:19:52: #1 total tags in treatment: 12837156 INFO @ Tue, 16 Jun 2020 09:19:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:52: #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 09:19:52: #1 tags after filtering in treatment: 12837156 INFO @ Tue, 16 Jun 2020 09:19:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:53: #2 number of paired peaks: 1582 INFO @ Tue, 16 Jun 2020 09:19:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:53: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 09:19:53: #2 alternative fragment length(s) may be 2,66,92 bps INFO @ Tue, 16 Jun 2020 09:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:53: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:53: #2 You may need to consider one of the other alternative d(s): 2,66,92 WARNING @ Tue, 16 Jun 2020 09:19:53: #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 09:19:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:56: 8000000 INFO @ Tue, 16 Jun 2020 09:19:57: 3000000 INFO @ Tue, 16 Jun 2020 09:20:03: 9000000 INFO @ Tue, 16 Jun 2020 09:20:03: 4000000 INFO @ Tue, 16 Jun 2020 09:20:09: 5000000 INFO @ Tue, 16 Jun 2020 09:20:09: 10000000 INFO @ Tue, 16 Jun 2020 09:20:15: 6000000 INFO @ Tue, 16 Jun 2020 09:20:15: 11000000 INFO @ Tue, 16 Jun 2020 09:20:21: 7000000 INFO @ Tue, 16 Jun 2020 09:20:21: 12000000 INFO @ Tue, 16 Jun 2020 09:20:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:26: #1 total tags in treatment: 12837156 INFO @ Tue, 16 Jun 2020 09:20:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:26: #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 09:20:26: #1 tags after filtering in treatment: 12837156 INFO @ Tue, 16 Jun 2020 09:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:27: 8000000 INFO @ Tue, 16 Jun 2020 09:20:27: #2 number of paired peaks: 1582 INFO @ Tue, 16 Jun 2020 09:20:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:27: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 09:20:27: #2 alternative fragment length(s) may be 2,66,92 bps INFO @ Tue, 16 Jun 2020 09:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:27: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:27: #2 You may need to consider one of the other alternative d(s): 2,66,92 WARNING @ Tue, 16 Jun 2020 09:20:27: #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 09:20:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:32: 9000000 INFO @ Tue, 16 Jun 2020 09:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1817 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:38: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:43: 11000000 INFO @ Tue, 16 Jun 2020 09:20:49: 12000000 INFO @ Tue, 16 Jun 2020 09:20:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:54: #1 total tags in treatment: 12837156 INFO @ Tue, 16 Jun 2020 09:20:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:54: #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 09:20:54: #1 tags after filtering in treatment: 12837156 INFO @ Tue, 16 Jun 2020 09:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:55: #2 number of paired peaks: 1582 INFO @ Tue, 16 Jun 2020 09:20:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:55: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 09:20:55: #2 alternative fragment length(s) may be 2,66,92 bps INFO @ Tue, 16 Jun 2020 09:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:55: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:55: #2 You may need to consider one of the other alternative d(s): 2,66,92 WARNING @ Tue, 16 Jun 2020 09:20:55: #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 09:20:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (708 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466462/SRX466462.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 1 millis CompletedMACS2peakCalling