Job ID = 6366099 SRX = SRX060165 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:37 prefetch.2.10.7: 1) Downloading 'SRR192330'... 2020-06-15T22:47:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:09 prefetch.2.10.7: 1) 'SRR192330' was downloaded successfully Read 19263987 spots for SRR192330/SRR192330.sra Written 19263987 spots for SRR192330/SRR192330.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: 00:03:48 19263987 reads; of these: 19263987 (100.00%) were unpaired; of these: 285930 (1.48%) aligned 0 times 15657817 (81.28%) aligned exactly 1 time 3320240 (17.24%) aligned >1 times 98.52% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 1890399 / 18978057 = 0.0996 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 07:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.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 07:59:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:11: 1000000 INFO @ Tue, 16 Jun 2020 07:59:16: 2000000 INFO @ Tue, 16 Jun 2020 07:59:22: 3000000 INFO @ Tue, 16 Jun 2020 07:59:27: 4000000 INFO @ Tue, 16 Jun 2020 07:59:32: 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 07:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.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 07:59:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:37: 6000000 INFO @ Tue, 16 Jun 2020 07:59:41: 1000000 INFO @ Tue, 16 Jun 2020 07:59:43: 7000000 INFO @ Tue, 16 Jun 2020 07:59:46: 2000000 INFO @ Tue, 16 Jun 2020 07:59:48: 8000000 INFO @ Tue, 16 Jun 2020 07:59:52: 3000000 INFO @ Tue, 16 Jun 2020 07:59:54: 9000000 INFO @ Tue, 16 Jun 2020 07:59:57: 4000000 INFO @ Tue, 16 Jun 2020 07:59:59: 10000000 INFO @ Tue, 16 Jun 2020 08:00:03: 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 08:00:05: 11000000 INFO @ Tue, 16 Jun 2020 08:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.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 08:00:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:08: 6000000 INFO @ Tue, 16 Jun 2020 08:00:11: 12000000 INFO @ Tue, 16 Jun 2020 08:00:11: 1000000 INFO @ Tue, 16 Jun 2020 08:00:14: 7000000 INFO @ Tue, 16 Jun 2020 08:00:16: 13000000 INFO @ Tue, 16 Jun 2020 08:00:17: 2000000 INFO @ Tue, 16 Jun 2020 08:00:19: 8000000 INFO @ Tue, 16 Jun 2020 08:00:22: 14000000 INFO @ Tue, 16 Jun 2020 08:00:23: 3000000 INFO @ Tue, 16 Jun 2020 08:00:25: 9000000 INFO @ Tue, 16 Jun 2020 08:00:27: 15000000 INFO @ Tue, 16 Jun 2020 08:00:28: 4000000 INFO @ Tue, 16 Jun 2020 08:00:30: 10000000 INFO @ Tue, 16 Jun 2020 08:00:33: 16000000 INFO @ Tue, 16 Jun 2020 08:00:34: 5000000 INFO @ Tue, 16 Jun 2020 08:00:36: 11000000 INFO @ Tue, 16 Jun 2020 08:00:38: 17000000 INFO @ Tue, 16 Jun 2020 08:00:39: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:00:39: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:00:39: #1 total tags in treatment: 17087658 INFO @ Tue, 16 Jun 2020 08:00:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:39: #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 08:00:39: #1 tags after filtering in treatment: 17087658 INFO @ Tue, 16 Jun 2020 08:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:39: 6000000 INFO @ Tue, 16 Jun 2020 08:00:40: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 08:00:40: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:00:40: #2 alternative fragment length(s) may be 1,21,517,531,562 bps INFO @ Tue, 16 Jun 2020 08:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.05_model.r WARNING @ Tue, 16 Jun 2020 08:00:40: #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 08:00:40: #2 You may need to consider one of the other alternative d(s): 1,21,517,531,562 WARNING @ Tue, 16 Jun 2020 08:00:40: #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 08:00:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:41: 12000000 INFO @ Tue, 16 Jun 2020 08:00:44: 7000000 INFO @ Tue, 16 Jun 2020 08:00:47: 13000000 INFO @ Tue, 16 Jun 2020 08:00:50: 8000000 INFO @ Tue, 16 Jun 2020 08:00:52: 14000000 INFO @ Tue, 16 Jun 2020 08:00:55: 9000000 INFO @ Tue, 16 Jun 2020 08:00:58: 15000000 INFO @ Tue, 16 Jun 2020 08:01:01: 10000000 INFO @ Tue, 16 Jun 2020 08:01:03: 16000000 INFO @ Tue, 16 Jun 2020 08:01:06: 11000000 INFO @ Tue, 16 Jun 2020 08:01:09: 17000000 INFO @ Tue, 16 Jun 2020 08:01:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:01:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:01:09: #1 total tags in treatment: 17087658 INFO @ Tue, 16 Jun 2020 08:01:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:09: #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 08:01:09: #1 tags after filtering in treatment: 17087658 INFO @ Tue, 16 Jun 2020 08:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:11: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 08:01:11: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:01:11: #2 alternative fragment length(s) may be 1,21,517,531,562 bps INFO @ Tue, 16 Jun 2020 08:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.10_model.r WARNING @ Tue, 16 Jun 2020 08:01:11: #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 08:01:11: #2 You may need to consider one of the other alternative d(s): 1,21,517,531,562 WARNING @ Tue, 16 Jun 2020 08:01:11: #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 08:01:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:12: 12000000 INFO @ Tue, 16 Jun 2020 08:01:17: 13000000 INFO @ Tue, 16 Jun 2020 08:01:22: 14000000 INFO @ Tue, 16 Jun 2020 08:01:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:01:33: 16000000 INFO @ Tue, 16 Jun 2020 08:01:38: 17000000 INFO @ Tue, 16 Jun 2020 08:01:38: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:01:38: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:01:38: #1 total tags in treatment: 17087658 INFO @ Tue, 16 Jun 2020 08:01:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:38: #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 08:01:39: #1 tags after filtering in treatment: 17087658 INFO @ Tue, 16 Jun 2020 08:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:40: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 08:01:40: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:01:40: #2 alternative fragment length(s) may be 1,21,517,531,562 bps INFO @ Tue, 16 Jun 2020 08:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.20_model.r WARNING @ Tue, 16 Jun 2020 08:01:40: #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 08:01:40: #2 You may need to consider one of the other alternative d(s): 1,21,517,531,562 WARNING @ Tue, 16 Jun 2020 08:01:40: #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 08:01:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:53: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX060165/SRX060165.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:22: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling