Job ID = 6368350 SRX = SRX495030 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:24 prefetch.2.10.7: 1) Downloading 'SRR1198562'... 2020-06-16T00:09:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:33 prefetch.2.10.7: 1) 'SRR1198562' was downloaded successfully Read 24434363 spots for SRR1198562/SRR1198562.sra Written 24434363 spots for SRR1198562/SRR1198562.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: 00:05:24 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3204916 (13.12%) aligned 0 times 17393290 (71.18%) aligned exactly 1 time 3836157 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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 12 files... [bam_rmdupse_core] 2473068 / 21229447 = 0.1165 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 09:25:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.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 09:25:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:59: 1000000 INFO @ Tue, 16 Jun 2020 09:26:04: 2000000 INFO @ Tue, 16 Jun 2020 09:26:10: 3000000 INFO @ Tue, 16 Jun 2020 09:26:15: 4000000 INFO @ Tue, 16 Jun 2020 09:26:21: 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 09:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.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 09:26:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:26: 6000000 INFO @ Tue, 16 Jun 2020 09:26:30: 1000000 INFO @ Tue, 16 Jun 2020 09:26:32: 7000000 INFO @ Tue, 16 Jun 2020 09:26:36: 2000000 INFO @ Tue, 16 Jun 2020 09:26:38: 8000000 INFO @ Tue, 16 Jun 2020 09:26:43: 3000000 INFO @ Tue, 16 Jun 2020 09:26:44: 9000000 INFO @ Tue, 16 Jun 2020 09:26:49: 4000000 INFO @ Tue, 16 Jun 2020 09:26:50: 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 09:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.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 09:26:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:55: 5000000 INFO @ Tue, 16 Jun 2020 09:26:56: 11000000 INFO @ Tue, 16 Jun 2020 09:27:00: 1000000 INFO @ Tue, 16 Jun 2020 09:27:02: 12000000 INFO @ Tue, 16 Jun 2020 09:27:02: 6000000 INFO @ Tue, 16 Jun 2020 09:27:07: 2000000 INFO @ Tue, 16 Jun 2020 09:27:08: 13000000 INFO @ Tue, 16 Jun 2020 09:27:09: 7000000 INFO @ Tue, 16 Jun 2020 09:27:13: 14000000 INFO @ Tue, 16 Jun 2020 09:27:13: 3000000 INFO @ Tue, 16 Jun 2020 09:27:15: 8000000 INFO @ Tue, 16 Jun 2020 09:27:19: 15000000 INFO @ Tue, 16 Jun 2020 09:27:20: 4000000 INFO @ Tue, 16 Jun 2020 09:27:22: 9000000 INFO @ Tue, 16 Jun 2020 09:27:25: 16000000 INFO @ Tue, 16 Jun 2020 09:27:26: 5000000 INFO @ Tue, 16 Jun 2020 09:27:29: 10000000 INFO @ Tue, 16 Jun 2020 09:27:31: 17000000 INFO @ Tue, 16 Jun 2020 09:27:33: 6000000 INFO @ Tue, 16 Jun 2020 09:27:36: 11000000 INFO @ Tue, 16 Jun 2020 09:27:36: 18000000 INFO @ Tue, 16 Jun 2020 09:27:40: 7000000 INFO @ Tue, 16 Jun 2020 09:27:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:27:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:27:41: #1 total tags in treatment: 18756379 INFO @ Tue, 16 Jun 2020 09:27:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:41: #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 09:27:41: #1 tags after filtering in treatment: 18756379 INFO @ Tue, 16 Jun 2020 09:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:43: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 09:27:43: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:43: 12000000 INFO @ Tue, 16 Jun 2020 09:27:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:27:43: #2 alternative fragment length(s) may be 1,14,35,46,536,553 bps INFO @ Tue, 16 Jun 2020 09:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.05_model.r WARNING @ Tue, 16 Jun 2020 09:27:43: #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 09:27:43: #2 You may need to consider one of the other alternative d(s): 1,14,35,46,536,553 WARNING @ Tue, 16 Jun 2020 09:27:43: #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 09:27:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:46: 8000000 INFO @ Tue, 16 Jun 2020 09:27:49: 13000000 INFO @ Tue, 16 Jun 2020 09:27:53: 9000000 INFO @ Tue, 16 Jun 2020 09:27:56: 14000000 INFO @ Tue, 16 Jun 2020 09:28:00: 10000000 INFO @ Tue, 16 Jun 2020 09:28:03: 15000000 INFO @ Tue, 16 Jun 2020 09:28:06: 11000000 INFO @ Tue, 16 Jun 2020 09:28:09: 16000000 INFO @ Tue, 16 Jun 2020 09:28:12: 12000000 INFO @ Tue, 16 Jun 2020 09:28:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:16: 17000000 INFO @ Tue, 16 Jun 2020 09:28:19: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:22: 18000000 INFO @ Tue, 16 Jun 2020 09:28:25: 14000000 INFO @ Tue, 16 Jun 2020 09:28:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:27: #1 total tags in treatment: 18756379 INFO @ Tue, 16 Jun 2020 09:28:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:27: #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 09:28:27: #1 tags after filtering in treatment: 18756379 INFO @ Tue, 16 Jun 2020 09:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:29: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 09:28:29: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:29: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:28:29: #2 alternative fragment length(s) may be 1,14,35,46,536,553 bps INFO @ Tue, 16 Jun 2020 09:28:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.10_model.r WARNING @ Tue, 16 Jun 2020 09:28:29: #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 09:28:29: #2 You may need to consider one of the other alternative d(s): 1,14,35,46,536,553 WARNING @ Tue, 16 Jun 2020 09:28:29: #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 09:28:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:31: 15000000 INFO @ Tue, 16 Jun 2020 09:28:37: 16000000 INFO @ Tue, 16 Jun 2020 09:28:44: 17000000 INFO @ Tue, 16 Jun 2020 09:28:50: 18000000 INFO @ Tue, 16 Jun 2020 09:28:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:54: #1 total tags in treatment: 18756379 INFO @ Tue, 16 Jun 2020 09:28:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:54: #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 09:28:55: #1 tags after filtering in treatment: 18756379 INFO @ Tue, 16 Jun 2020 09:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 09:28:56: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2 alternative fragment length(s) may be 1,14,35,46,536,553 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.20_model.r WARNING @ Tue, 16 Jun 2020 09:28:56: #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 09:28:56: #2 You may need to consider one of the other alternative d(s): 1,14,35,46,536,553 WARNING @ Tue, 16 Jun 2020 09:28:56: #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 09:28:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495030/SRX495030.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling