Job ID = 6368753 SRX = SRX5545238 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:37:35 prefetch.2.10.7: 1) Downloading 'SRR8754477'... 2020-06-16T00:37:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:37 prefetch.2.10.7: 1) 'SRR8754477' was downloaded successfully 2020-06-16T00:39:37 prefetch.2.10.7: 'SRR8754477' has 0 unresolved dependencies Read 33377549 spots for SRR8754477/SRR8754477.sra Written 33377549 spots for SRR8754477/SRR8754477.sra 2020-06-16T00:41:55 prefetch.2.10.7: 1) Downloading 'SRR8754478'... 2020-06-16T00:41:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:54 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:54 prefetch.2.10.7: 1) 'SRR8754478' was downloaded successfully 2020-06-16T00:46:54 prefetch.2.10.7: 'SRR8754478' has 0 unresolved dependencies Read 52862300 spots for SRR8754478/SRR8754478.sra Written 52862300 spots for SRR8754478/SRR8754478.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: 00:15:14 86239849 reads; of these: 86239849 (100.00%) were unpaired; of these: 24393586 (28.29%) aligned 0 times 51262236 (59.44%) aligned exactly 1 time 10584027 (12.27%) aligned >1 times 71.71% overall alignment rate Time searching: 00:15:14 Overall time: 00:15:14 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 28 files... [bam_rmdupse_core] 32897954 / 61846263 = 0.5319 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 10:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.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 10:16:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:16:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:17:03: 1000000 INFO @ Tue, 16 Jun 2020 10:17:11: 2000000 INFO @ Tue, 16 Jun 2020 10:17:18: 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 10:17:26: 4000000 INFO @ Tue, 16 Jun 2020 10:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.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 10:17:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:17:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:17:35: 5000000 INFO @ Tue, 16 Jun 2020 10:17:36: 1000000 INFO @ Tue, 16 Jun 2020 10:17:43: 6000000 INFO @ Tue, 16 Jun 2020 10:17:45: 2000000 INFO @ Tue, 16 Jun 2020 10:17:52: 7000000 INFO @ Tue, 16 Jun 2020 10:17:54: 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 10:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.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 10:17:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:17:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:18:01: 8000000 INFO @ Tue, 16 Jun 2020 10:18:03: 4000000 INFO @ Tue, 16 Jun 2020 10:18:04: 1000000 INFO @ Tue, 16 Jun 2020 10:18:10: 9000000 INFO @ Tue, 16 Jun 2020 10:18:11: 2000000 INFO @ Tue, 16 Jun 2020 10:18:13: 5000000 INFO @ Tue, 16 Jun 2020 10:18:19: 3000000 INFO @ Tue, 16 Jun 2020 10:18:20: 10000000 INFO @ Tue, 16 Jun 2020 10:18:23: 6000000 INFO @ Tue, 16 Jun 2020 10:18:26: 4000000 INFO @ Tue, 16 Jun 2020 10:18:30: 11000000 INFO @ Tue, 16 Jun 2020 10:18:32: 7000000 INFO @ Tue, 16 Jun 2020 10:18:34: 5000000 INFO @ Tue, 16 Jun 2020 10:18:39: 12000000 INFO @ Tue, 16 Jun 2020 10:18:41: 6000000 INFO @ Tue, 16 Jun 2020 10:18:42: 8000000 INFO @ Tue, 16 Jun 2020 10:18:49: 7000000 INFO @ Tue, 16 Jun 2020 10:18:49: 13000000 INFO @ Tue, 16 Jun 2020 10:18:51: 9000000 INFO @ Tue, 16 Jun 2020 10:18:56: 8000000 INFO @ Tue, 16 Jun 2020 10:18:59: 14000000 INFO @ Tue, 16 Jun 2020 10:19:01: 10000000 INFO @ Tue, 16 Jun 2020 10:19:04: 9000000 INFO @ Tue, 16 Jun 2020 10:19:08: 15000000 INFO @ Tue, 16 Jun 2020 10:19:11: 11000000 INFO @ Tue, 16 Jun 2020 10:19:11: 10000000 INFO @ Tue, 16 Jun 2020 10:19:18: 16000000 INFO @ Tue, 16 Jun 2020 10:19:19: 11000000 INFO @ Tue, 16 Jun 2020 10:19:20: 12000000 INFO @ Tue, 16 Jun 2020 10:19:27: 12000000 INFO @ Tue, 16 Jun 2020 10:19:28: 17000000 INFO @ Tue, 16 Jun 2020 10:19:30: 13000000 INFO @ Tue, 16 Jun 2020 10:19:35: 13000000 INFO @ Tue, 16 Jun 2020 10:19:37: 18000000 INFO @ Tue, 16 Jun 2020 10:19:40: 14000000 INFO @ Tue, 16 Jun 2020 10:19:43: 14000000 INFO @ Tue, 16 Jun 2020 10:19:47: 19000000 INFO @ Tue, 16 Jun 2020 10:19:49: 15000000 INFO @ Tue, 16 Jun 2020 10:19:50: 15000000 INFO @ Tue, 16 Jun 2020 10:19:56: 20000000 INFO @ Tue, 16 Jun 2020 10:19:59: 16000000 INFO @ Tue, 16 Jun 2020 10:19:59: 16000000 INFO @ Tue, 16 Jun 2020 10:20:06: 21000000 INFO @ Tue, 16 Jun 2020 10:20:07: 17000000 INFO @ Tue, 16 Jun 2020 10:20:08: 17000000 INFO @ Tue, 16 Jun 2020 10:20:14: 18000000 INFO @ Tue, 16 Jun 2020 10:20:16: 22000000 INFO @ Tue, 16 Jun 2020 10:20:18: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:20:22: 19000000 INFO @ Tue, 16 Jun 2020 10:20:25: 23000000 INFO @ Tue, 16 Jun 2020 10:20:28: 19000000 INFO @ Tue, 16 Jun 2020 10:20:30: 20000000 INFO @ Tue, 16 Jun 2020 10:20:35: 24000000 INFO @ Tue, 16 Jun 2020 10:20:37: 20000000 INFO @ Tue, 16 Jun 2020 10:20:37: 21000000 INFO @ Tue, 16 Jun 2020 10:20:44: 25000000 INFO @ Tue, 16 Jun 2020 10:20:45: 22000000 INFO @ Tue, 16 Jun 2020 10:20:47: 21000000 INFO @ Tue, 16 Jun 2020 10:20:52: 23000000 INFO @ Tue, 16 Jun 2020 10:20:54: 26000000 INFO @ Tue, 16 Jun 2020 10:20:56: 22000000 INFO @ Tue, 16 Jun 2020 10:21:00: 24000000 INFO @ Tue, 16 Jun 2020 10:21:03: 27000000 INFO @ Tue, 16 Jun 2020 10:21:06: 23000000 INFO @ Tue, 16 Jun 2020 10:21:07: 25000000 INFO @ Tue, 16 Jun 2020 10:21:13: 28000000 INFO @ Tue, 16 Jun 2020 10:21:14: 26000000 INFO @ Tue, 16 Jun 2020 10:21:15: 24000000 INFO @ Tue, 16 Jun 2020 10:21:21: 27000000 INFO @ Tue, 16 Jun 2020 10:21:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:21:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:21:21: #1 total tags in treatment: 28948309 INFO @ Tue, 16 Jun 2020 10:21:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:21:21: #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 10:21:22: #1 tags after filtering in treatment: 28948309 INFO @ Tue, 16 Jun 2020 10:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:21:22: #1 finished! INFO @ Tue, 16 Jun 2020 10:21:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:21:23: #2 number of paired peaks: 244 WARNING @ Tue, 16 Jun 2020 10:21:23: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 16 Jun 2020 10:21:23: start model_add_line... INFO @ Tue, 16 Jun 2020 10:21:24: start X-correlation... INFO @ Tue, 16 Jun 2020 10:21:24: end of X-cor INFO @ Tue, 16 Jun 2020 10:21:24: #2 finished! INFO @ Tue, 16 Jun 2020 10:21:24: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 10:21:24: #2 alternative fragment length(s) may be 2,28,48 bps INFO @ Tue, 16 Jun 2020 10:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.05_model.r WARNING @ Tue, 16 Jun 2020 10:21:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:21:24: #2 You may need to consider one of the other alternative d(s): 2,28,48 WARNING @ Tue, 16 Jun 2020 10:21:24: #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 10:21:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:21:24: 25000000 INFO @ Tue, 16 Jun 2020 10:21:28: 28000000 INFO @ Tue, 16 Jun 2020 10:21:33: 26000000 INFO @ Tue, 16 Jun 2020 10:21:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:21:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:21:34: #1 total tags in treatment: 28948309 INFO @ Tue, 16 Jun 2020 10:21:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:21:34: #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 10:21:35: #1 tags after filtering in treatment: 28948309 INFO @ Tue, 16 Jun 2020 10:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:21:35: #1 finished! INFO @ Tue, 16 Jun 2020 10:21:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:21:35: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:21:37: #2 number of paired peaks: 244 WARNING @ Tue, 16 Jun 2020 10:21:37: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 16 Jun 2020 10:21:37: start model_add_line... INFO @ Tue, 16 Jun 2020 10:21:37: start X-correlation... INFO @ Tue, 16 Jun 2020 10:21:37: end of X-cor INFO @ Tue, 16 Jun 2020 10:21:37: #2 finished! INFO @ Tue, 16 Jun 2020 10:21:37: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 10:21:37: #2 alternative fragment length(s) may be 2,28,48 bps INFO @ Tue, 16 Jun 2020 10:21:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.20_model.r WARNING @ Tue, 16 Jun 2020 10:21:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:21:37: #2 You may need to consider one of the other alternative d(s): 2,28,48 WARNING @ Tue, 16 Jun 2020 10:21:37: #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 10:21:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:21:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:21:42: 27000000 INFO @ Tue, 16 Jun 2020 10:21:51: 28000000 INFO @ Tue, 16 Jun 2020 10:21:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:21:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:21:59: #1 total tags in treatment: 28948309 INFO @ Tue, 16 Jun 2020 10:21:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:21:59: #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 10:22:00: #1 tags after filtering in treatment: 28948309 INFO @ Tue, 16 Jun 2020 10:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:22:00: #1 finished! INFO @ Tue, 16 Jun 2020 10:22:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:22:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:22:01: #2 number of paired peaks: 244 WARNING @ Tue, 16 Jun 2020 10:22:01: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Tue, 16 Jun 2020 10:22:01: start model_add_line... INFO @ Tue, 16 Jun 2020 10:22:02: start X-correlation... INFO @ Tue, 16 Jun 2020 10:22:02: end of X-cor INFO @ Tue, 16 Jun 2020 10:22:02: #2 finished! INFO @ Tue, 16 Jun 2020 10:22:02: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 10:22:02: #2 alternative fragment length(s) may be 2,28,48 bps INFO @ Tue, 16 Jun 2020 10:22:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.10_model.r WARNING @ Tue, 16 Jun 2020 10:22:02: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:22:02: #2 You may need to consider one of the other alternative d(s): 2,28,48 WARNING @ Tue, 16 Jun 2020 10:22:02: #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 10:22:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:22:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:22:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.05_summits.bed INFO @ Tue, 16 Jun 2020 10:22:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:22:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:22:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.20_summits.bed INFO @ Tue, 16 Jun 2020 10:22:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545238/SRX5545238.10_summits.bed INFO @ Tue, 16 Jun 2020 10:22:56: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling