Job ID = 6368092 SRX = SRX466555 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:59:20 prefetch.2.10.7: 1) Downloading 'SRR1163621'... 2020-06-15T23:59:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:09 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:09 prefetch.2.10.7: 1) 'SRR1163621' was downloaded successfully Read 30788149 spots for SRR1163621/SRR1163621.sra Written 30788149 spots for SRR1163621/SRR1163621.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: 00:05:18 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169823 (0.55%) aligned 0 times 25275324 (82.09%) aligned exactly 1 time 5343002 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 4711057 / 30618326 = 0.1539 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 09:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.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 09:14:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:23: 1000000 INFO @ Tue, 16 Jun 2020 09:14:28: 2000000 INFO @ Tue, 16 Jun 2020 09:14:33: 3000000 INFO @ Tue, 16 Jun 2020 09:14:38: 4000000 INFO @ Tue, 16 Jun 2020 09:14:43: 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 09:14:48: 6000000 INFO @ Tue, 16 Jun 2020 09:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.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 09:14:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:53: 7000000 INFO @ Tue, 16 Jun 2020 09:14:53: 1000000 INFO @ Tue, 16 Jun 2020 09:14:59: 8000000 INFO @ Tue, 16 Jun 2020 09:14:59: 2000000 INFO @ Tue, 16 Jun 2020 09:15:04: 9000000 INFO @ Tue, 16 Jun 2020 09:15:04: 3000000 INFO @ Tue, 16 Jun 2020 09:15:09: 10000000 INFO @ Tue, 16 Jun 2020 09:15:09: 4000000 INFO @ Tue, 16 Jun 2020 09:15:15: 11000000 INFO @ Tue, 16 Jun 2020 09:15:15: 5000000 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 09:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.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 09:15:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:20: 12000000 INFO @ Tue, 16 Jun 2020 09:15:20: 6000000 INFO @ Tue, 16 Jun 2020 09:15:24: 1000000 INFO @ Tue, 16 Jun 2020 09:15:26: 7000000 INFO @ Tue, 16 Jun 2020 09:15:26: 13000000 INFO @ Tue, 16 Jun 2020 09:15:29: 2000000 INFO @ Tue, 16 Jun 2020 09:15:31: 8000000 INFO @ Tue, 16 Jun 2020 09:15:31: 14000000 INFO @ Tue, 16 Jun 2020 09:15:35: 3000000 INFO @ Tue, 16 Jun 2020 09:15:37: 9000000 INFO @ Tue, 16 Jun 2020 09:15:37: 15000000 INFO @ Tue, 16 Jun 2020 09:15:40: 4000000 INFO @ Tue, 16 Jun 2020 09:15:42: 10000000 INFO @ Tue, 16 Jun 2020 09:15:43: 16000000 INFO @ Tue, 16 Jun 2020 09:15:46: 5000000 INFO @ Tue, 16 Jun 2020 09:15:48: 11000000 INFO @ Tue, 16 Jun 2020 09:15:48: 17000000 INFO @ Tue, 16 Jun 2020 09:15:51: 6000000 INFO @ Tue, 16 Jun 2020 09:15:53: 12000000 INFO @ Tue, 16 Jun 2020 09:15:54: 18000000 INFO @ Tue, 16 Jun 2020 09:15:57: 7000000 INFO @ Tue, 16 Jun 2020 09:15:59: 13000000 INFO @ Tue, 16 Jun 2020 09:16:00: 19000000 INFO @ Tue, 16 Jun 2020 09:16:02: 8000000 INFO @ Tue, 16 Jun 2020 09:16:04: 14000000 INFO @ Tue, 16 Jun 2020 09:16:06: 20000000 INFO @ Tue, 16 Jun 2020 09:16:08: 9000000 INFO @ Tue, 16 Jun 2020 09:16:10: 15000000 INFO @ Tue, 16 Jun 2020 09:16:11: 21000000 INFO @ Tue, 16 Jun 2020 09:16:13: 10000000 INFO @ Tue, 16 Jun 2020 09:16:15: 16000000 INFO @ Tue, 16 Jun 2020 09:16:17: 22000000 INFO @ Tue, 16 Jun 2020 09:16:19: 11000000 INFO @ Tue, 16 Jun 2020 09:16:21: 17000000 INFO @ Tue, 16 Jun 2020 09:16:22: 23000000 INFO @ Tue, 16 Jun 2020 09:16:24: 12000000 INFO @ Tue, 16 Jun 2020 09:16:26: 18000000 INFO @ Tue, 16 Jun 2020 09:16:28: 24000000 INFO @ Tue, 16 Jun 2020 09:16:30: 13000000 INFO @ Tue, 16 Jun 2020 09:16:32: 19000000 INFO @ Tue, 16 Jun 2020 09:16:34: 25000000 INFO @ Tue, 16 Jun 2020 09:16:35: 14000000 INFO @ Tue, 16 Jun 2020 09:16:37: 20000000 INFO @ Tue, 16 Jun 2020 09:16:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:16:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:16:39: #1 total tags in treatment: 25907269 INFO @ Tue, 16 Jun 2020 09:16:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:39: #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 09:16:39: #1 tags after filtering in treatment: 25907269 INFO @ Tue, 16 Jun 2020 09:16:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:41: 15000000 INFO @ Tue, 16 Jun 2020 09:16:41: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:16:41: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:41: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:16:41: #2 alternative fragment length(s) may be 1,450,524,538,558,576 bps INFO @ Tue, 16 Jun 2020 09:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:41: #2 You may need to consider one of the other alternative d(s): 1,450,524,538,558,576 WARNING @ Tue, 16 Jun 2020 09:16:41: #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 09:16:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:43: 21000000 INFO @ Tue, 16 Jun 2020 09:16:46: 16000000 INFO @ Tue, 16 Jun 2020 09:16:48: 22000000 INFO @ Tue, 16 Jun 2020 09:16:51: 17000000 INFO @ Tue, 16 Jun 2020 09:16:53: 23000000 INFO @ Tue, 16 Jun 2020 09:16:57: 18000000 INFO @ Tue, 16 Jun 2020 09:16:59: 24000000 INFO @ Tue, 16 Jun 2020 09:17:02: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:04: 25000000 INFO @ Tue, 16 Jun 2020 09:17:08: 20000000 INFO @ Tue, 16 Jun 2020 09:17:10: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:17:10: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:17:10: #1 total tags in treatment: 25907269 INFO @ Tue, 16 Jun 2020 09:17:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:10: #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 09:17:10: #1 tags after filtering in treatment: 25907269 INFO @ Tue, 16 Jun 2020 09:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:12: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:17:12: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:12: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:17:12: #2 alternative fragment length(s) may be 1,450,524,538,558,576 bps INFO @ Tue, 16 Jun 2020 09:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:12: #2 You may need to consider one of the other alternative d(s): 1,450,524,538,558,576 WARNING @ Tue, 16 Jun 2020 09:17:12: #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 09:17:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:14: 21000000 INFO @ Tue, 16 Jun 2020 09:17:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:19: 22000000 INFO @ Tue, 16 Jun 2020 09:17:24: 23000000 INFO @ Tue, 16 Jun 2020 09:17:29: 24000000 INFO @ Tue, 16 Jun 2020 09:17:34: 25000000 INFO @ Tue, 16 Jun 2020 09:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:17:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:17:39: #1 total tags in treatment: 25907269 INFO @ Tue, 16 Jun 2020 09:17:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:39: #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 09:17:40: #1 tags after filtering in treatment: 25907269 INFO @ Tue, 16 Jun 2020 09:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:41: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:17:41: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:41: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:17:41: #2 alternative fragment length(s) may be 1,450,524,538,558,576 bps INFO @ Tue, 16 Jun 2020 09:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:41: #2 You may need to consider one of the other alternative d(s): 1,450,524,538,558,576 WARNING @ Tue, 16 Jun 2020 09:17:41: #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 09:17:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.10_summits.bed INFO @ Tue, 16 Jun 2020 09:18:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:18:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466555/SRX466555.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:37: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling