Job ID = 6368064 SRX = SRX466527 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:49:33 prefetch.2.10.7: 1) Downloading 'SRR1163593'... 2020-06-15T23:49:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:22 prefetch.2.10.7: 1) 'SRR1163593' was downloaded successfully Read 30788149 spots for SRR1163593/SRR1163593.sra Written 30788149 spots for SRR1163593/SRR1163593.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: 00:05:21 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169809 (0.55%) aligned 0 times 25275427 (82.09%) aligned exactly 1 time 5342913 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 4711700 / 30618340 = 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 09:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.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 09:05:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:34: 1000000 INFO @ Tue, 16 Jun 2020 09:05:39: 2000000 INFO @ Tue, 16 Jun 2020 09:05:44: 3000000 INFO @ Tue, 16 Jun 2020 09:05:49: 4000000 INFO @ Tue, 16 Jun 2020 09:05:54: 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 09:05:59: 6000000 INFO @ Tue, 16 Jun 2020 09:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.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 09:05:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:04: 7000000 INFO @ Tue, 16 Jun 2020 09:06:04: 1000000 INFO @ Tue, 16 Jun 2020 09:06:09: 8000000 INFO @ Tue, 16 Jun 2020 09:06:10: 2000000 INFO @ Tue, 16 Jun 2020 09:06:15: 9000000 INFO @ Tue, 16 Jun 2020 09:06:15: 3000000 INFO @ Tue, 16 Jun 2020 09:06:20: 10000000 INFO @ Tue, 16 Jun 2020 09:06:20: 4000000 INFO @ Tue, 16 Jun 2020 09:06:25: 11000000 INFO @ Tue, 16 Jun 2020 09:06:25: 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 09:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.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 09:06:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:31: 12000000 INFO @ Tue, 16 Jun 2020 09:06:31: 6000000 INFO @ Tue, 16 Jun 2020 09:06:36: 1000000 INFO @ Tue, 16 Jun 2020 09:06:36: 13000000 INFO @ Tue, 16 Jun 2020 09:06:37: 7000000 INFO @ Tue, 16 Jun 2020 09:06:42: 14000000 INFO @ Tue, 16 Jun 2020 09:06:42: 2000000 INFO @ Tue, 16 Jun 2020 09:06:43: 8000000 INFO @ Tue, 16 Jun 2020 09:06:48: 15000000 INFO @ Tue, 16 Jun 2020 09:06:49: 9000000 INFO @ Tue, 16 Jun 2020 09:06:49: 3000000 INFO @ Tue, 16 Jun 2020 09:06:54: 16000000 INFO @ Tue, 16 Jun 2020 09:06:54: 10000000 INFO @ Tue, 16 Jun 2020 09:06:56: 4000000 INFO @ Tue, 16 Jun 2020 09:06:59: 17000000 INFO @ Tue, 16 Jun 2020 09:07:00: 11000000 INFO @ Tue, 16 Jun 2020 09:07:03: 5000000 INFO @ Tue, 16 Jun 2020 09:07:05: 18000000 INFO @ Tue, 16 Jun 2020 09:07:06: 12000000 INFO @ Tue, 16 Jun 2020 09:07:10: 6000000 INFO @ Tue, 16 Jun 2020 09:07:11: 19000000 INFO @ Tue, 16 Jun 2020 09:07:12: 13000000 INFO @ Tue, 16 Jun 2020 09:07:16: 7000000 INFO @ Tue, 16 Jun 2020 09:07:17: 20000000 INFO @ Tue, 16 Jun 2020 09:07:18: 14000000 INFO @ Tue, 16 Jun 2020 09:07:23: 21000000 INFO @ Tue, 16 Jun 2020 09:07:23: 8000000 INFO @ Tue, 16 Jun 2020 09:07:24: 15000000 INFO @ Tue, 16 Jun 2020 09:07:28: 22000000 INFO @ Tue, 16 Jun 2020 09:07:29: 9000000 INFO @ Tue, 16 Jun 2020 09:07:30: 16000000 INFO @ Tue, 16 Jun 2020 09:07:34: 23000000 INFO @ Tue, 16 Jun 2020 09:07:35: 17000000 INFO @ Tue, 16 Jun 2020 09:07:35: 10000000 INFO @ Tue, 16 Jun 2020 09:07:40: 24000000 INFO @ Tue, 16 Jun 2020 09:07:42: 18000000 INFO @ Tue, 16 Jun 2020 09:07:42: 11000000 INFO @ Tue, 16 Jun 2020 09:07:46: 25000000 INFO @ Tue, 16 Jun 2020 09:07:48: 19000000 INFO @ Tue, 16 Jun 2020 09:07:48: 12000000 INFO @ Tue, 16 Jun 2020 09:07:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:07:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:07:52: #1 total tags in treatment: 25906640 INFO @ Tue, 16 Jun 2020 09:07:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:52: #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 09:07:52: #1 tags after filtering in treatment: 25906640 INFO @ Tue, 16 Jun 2020 09:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:53: 20000000 INFO @ Tue, 16 Jun 2020 09:07:54: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:07:54: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:07:54: #2 alternative fragment length(s) may be 1,18,34,495,499,560,577,579 bps INFO @ Tue, 16 Jun 2020 09:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.05_model.r WARNING @ Tue, 16 Jun 2020 09:07:54: #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 09:07:54: #2 You may need to consider one of the other alternative d(s): 1,18,34,495,499,560,577,579 WARNING @ Tue, 16 Jun 2020 09:07:54: #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 09:07:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:54: 13000000 INFO @ Tue, 16 Jun 2020 09:07:59: 21000000 INFO @ Tue, 16 Jun 2020 09:08:01: 14000000 INFO @ Tue, 16 Jun 2020 09:08:05: 22000000 INFO @ Tue, 16 Jun 2020 09:08:07: 15000000 INFO @ Tue, 16 Jun 2020 09:08:11: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:13: 16000000 INFO @ Tue, 16 Jun 2020 09:08:17: 24000000 INFO @ Tue, 16 Jun 2020 09:08:19: 17000000 INFO @ Tue, 16 Jun 2020 09:08:23: 25000000 INFO @ Tue, 16 Jun 2020 09:08:26: 18000000 INFO @ Tue, 16 Jun 2020 09:08:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:08:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:08:28: #1 total tags in treatment: 25906640 INFO @ Tue, 16 Jun 2020 09:08:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:28: #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 09:08:29: #1 tags after filtering in treatment: 25906640 INFO @ Tue, 16 Jun 2020 09:08:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:31: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:08:31: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:08:31: #2 alternative fragment length(s) may be 1,18,34,495,499,560,577,579 bps INFO @ Tue, 16 Jun 2020 09:08:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.10_model.r WARNING @ Tue, 16 Jun 2020 09:08:31: #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 09:08:31: #2 You may need to consider one of the other alternative d(s): 1,18,34,495,499,560,577,579 WARNING @ Tue, 16 Jun 2020 09:08:31: #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 09:08:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:32: 19000000 INFO @ Tue, 16 Jun 2020 09:08:38: 20000000 INFO @ Tue, 16 Jun 2020 09:08:44: 21000000 INFO @ Tue, 16 Jun 2020 09:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.05_summits.bed INFO @ Tue, 16 Jun 2020 09:08:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:49: 22000000 INFO @ Tue, 16 Jun 2020 09:08:55: 23000000 INFO @ Tue, 16 Jun 2020 09:09:01: 24000000 INFO @ Tue, 16 Jun 2020 09:09:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:09:07: 25000000 INFO @ Tue, 16 Jun 2020 09:09:12: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:09:12: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:09:12: #1 total tags in treatment: 25906640 INFO @ Tue, 16 Jun 2020 09:09:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:12: #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 09:09:12: #1 tags after filtering in treatment: 25906640 INFO @ Tue, 16 Jun 2020 09:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:14: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:09:14: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:14: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:09:14: #2 alternative fragment length(s) may be 1,18,34,495,499,560,577,579 bps INFO @ Tue, 16 Jun 2020 09:09:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:14: #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 09:09:14: #2 You may need to consider one of the other alternative d(s): 1,18,34,495,499,560,577,579 WARNING @ Tue, 16 Jun 2020 09:09:14: #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 09:09:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.10_summits.bed INFO @ Tue, 16 Jun 2020 09:09:23: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466527/SRX466527.20_summits.bed INFO @ Tue, 16 Jun 2020 09:10:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling