Job ID = 6527418 SRX = SRX5402769 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:30:08 prefetch.2.10.7: 1) Downloading 'SRR8603003'... 2020-06-29T12:30:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:34:07 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:34:07 prefetch.2.10.7: 1) 'SRR8603003' was downloaded successfully Read 27498817 spots for SRR8603003/SRR8603003.sra Written 27498817 spots for SRR8603003/SRR8603003.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: 00:05:57 27498817 reads; of these: 27498817 (100.00%) were unpaired; of these: 1202302 (4.37%) aligned 0 times 21845406 (79.44%) aligned exactly 1 time 4451109 (16.19%) aligned >1 times 95.63% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 9412896 / 26296515 = 0.3580 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 @ Mon, 29 Jun 2020 21:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.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 @ Mon, 29 Jun 2020 21:53:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:53:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:53:20: 1000000 INFO @ Mon, 29 Jun 2020 21:53:27: 2000000 INFO @ Mon, 29 Jun 2020 21:53:33: 3000000 INFO @ Mon, 29 Jun 2020 21:53:39: 4000000 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 @ Mon, 29 Jun 2020 21:53:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.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 @ Mon, 29 Jun 2020 21:53:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:53:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:53:45: 5000000 INFO @ Mon, 29 Jun 2020 21:53:51: 1000000 INFO @ Mon, 29 Jun 2020 21:53:52: 6000000 INFO @ Mon, 29 Jun 2020 21:53:57: 2000000 INFO @ Mon, 29 Jun 2020 21:53:58: 7000000 INFO @ Mon, 29 Jun 2020 21:54:04: 3000000 INFO @ Mon, 29 Jun 2020 21:54:05: 8000000 INFO @ Mon, 29 Jun 2020 21:54:10: 4000000 INFO @ Mon, 29 Jun 2020 21:54:12: 9000000 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 @ Mon, 29 Jun 2020 21:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.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 @ Mon, 29 Jun 2020 21:54:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:54:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:54:17: 5000000 INFO @ Mon, 29 Jun 2020 21:54:18: 10000000 INFO @ Mon, 29 Jun 2020 21:54:21: 1000000 INFO @ Mon, 29 Jun 2020 21:54:24: 6000000 INFO @ Mon, 29 Jun 2020 21:54:25: 11000000 INFO @ Mon, 29 Jun 2020 21:54:28: 2000000 INFO @ Mon, 29 Jun 2020 21:54:31: 7000000 INFO @ Mon, 29 Jun 2020 21:54:32: 12000000 INFO @ Mon, 29 Jun 2020 21:54:36: 3000000 INFO @ Mon, 29 Jun 2020 21:54:38: 8000000 INFO @ Mon, 29 Jun 2020 21:54:39: 13000000 INFO @ Mon, 29 Jun 2020 21:54:43: 4000000 INFO @ Mon, 29 Jun 2020 21:54:45: 9000000 INFO @ Mon, 29 Jun 2020 21:54:46: 14000000 INFO @ Mon, 29 Jun 2020 21:54:50: 5000000 INFO @ Mon, 29 Jun 2020 21:54:52: 15000000 INFO @ Mon, 29 Jun 2020 21:54:53: 10000000 INFO @ Mon, 29 Jun 2020 21:54:57: 6000000 INFO @ Mon, 29 Jun 2020 21:54:59: 16000000 INFO @ Mon, 29 Jun 2020 21:55:00: 11000000 INFO @ Mon, 29 Jun 2020 21:55:04: 7000000 INFO @ Mon, 29 Jun 2020 21:55:05: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:55:05: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:55:05: #1 total tags in treatment: 16883619 INFO @ Mon, 29 Jun 2020 21:55:05: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:55:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:55:06: #1 tags after filtering in treatment: 16883619 INFO @ Mon, 29 Jun 2020 21:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:55:06: #1 finished! INFO @ Mon, 29 Jun 2020 21:55:06: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:55:07: #2 number of paired peaks: 328 WARNING @ Mon, 29 Jun 2020 21:55:07: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Mon, 29 Jun 2020 21:55:07: start model_add_line... INFO @ Mon, 29 Jun 2020 21:55:07: start X-correlation... INFO @ Mon, 29 Jun 2020 21:55:07: end of X-cor INFO @ Mon, 29 Jun 2020 21:55:07: #2 finished! INFO @ Mon, 29 Jun 2020 21:55:07: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:55:07: #2 alternative fragment length(s) may be 1,46,558,577 bps INFO @ Mon, 29 Jun 2020 21:55:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.05_model.r WARNING @ Mon, 29 Jun 2020 21:55:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:55:07: #2 You may need to consider one of the other alternative d(s): 1,46,558,577 WARNING @ Mon, 29 Jun 2020 21:55:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:55:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:55:07: 12000000 INFO @ Mon, 29 Jun 2020 21:55:11: 8000000 INFO @ Mon, 29 Jun 2020 21:55:13: 13000000 INFO @ Mon, 29 Jun 2020 21:55:18: 9000000 INFO @ Mon, 29 Jun 2020 21:55:20: 14000000 INFO @ Mon, 29 Jun 2020 21:55:25: 10000000 INFO @ Mon, 29 Jun 2020 21:55:27: 15000000 INFO @ Mon, 29 Jun 2020 21:55:32: 11000000 INFO @ Mon, 29 Jun 2020 21:55:34: 16000000 INFO @ Mon, 29 Jun 2020 21:55:35: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:55:39: 12000000 INFO @ Mon, 29 Jun 2020 21:55:40: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:55:40: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:55:40: #1 total tags in treatment: 16883619 INFO @ Mon, 29 Jun 2020 21:55:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:55:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:55:40: #1 tags after filtering in treatment: 16883619 INFO @ Mon, 29 Jun 2020 21:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:55:40: #1 finished! INFO @ Mon, 29 Jun 2020 21:55:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:55:41: #2 number of paired peaks: 328 WARNING @ Mon, 29 Jun 2020 21:55:41: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Mon, 29 Jun 2020 21:55:41: start model_add_line... INFO @ Mon, 29 Jun 2020 21:55:41: start X-correlation... INFO @ Mon, 29 Jun 2020 21:55:41: end of X-cor INFO @ Mon, 29 Jun 2020 21:55:41: #2 finished! INFO @ Mon, 29 Jun 2020 21:55:41: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:55:41: #2 alternative fragment length(s) may be 1,46,558,577 bps INFO @ Mon, 29 Jun 2020 21:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.10_model.r WARNING @ Mon, 29 Jun 2020 21:55:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:55:41: #2 You may need to consider one of the other alternative d(s): 1,46,558,577 WARNING @ Mon, 29 Jun 2020 21:55:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:55:41: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:55:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:55:45: 13000000 INFO @ Mon, 29 Jun 2020 21:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.05_summits.bed INFO @ Mon, 29 Jun 2020 21:55:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:55:51: 14000000 INFO @ Mon, 29 Jun 2020 21:55:57: 15000000 INFO @ Mon, 29 Jun 2020 21:56:03: 16000000 INFO @ Mon, 29 Jun 2020 21:56:09: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:56:09: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:56:09: #1 total tags in treatment: 16883619 INFO @ Mon, 29 Jun 2020 21:56:09: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:56:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:56:09: #1 tags after filtering in treatment: 16883619 INFO @ Mon, 29 Jun 2020 21:56:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:56:09: #1 finished! INFO @ Mon, 29 Jun 2020 21:56:09: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:56:09: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:56:10: #2 number of paired peaks: 328 WARNING @ Mon, 29 Jun 2020 21:56:10: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Mon, 29 Jun 2020 21:56:10: start model_add_line... INFO @ Mon, 29 Jun 2020 21:56:10: start X-correlation... INFO @ Mon, 29 Jun 2020 21:56:10: end of X-cor INFO @ Mon, 29 Jun 2020 21:56:10: #2 finished! INFO @ Mon, 29 Jun 2020 21:56:10: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:56:10: #2 alternative fragment length(s) may be 1,46,558,577 bps INFO @ Mon, 29 Jun 2020 21:56:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.20_model.r WARNING @ Mon, 29 Jun 2020 21:56:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:56:10: #2 You may need to consider one of the other alternative d(s): 1,46,558,577 WARNING @ Mon, 29 Jun 2020 21:56:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:56:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:56:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.10_summits.bed INFO @ Mon, 29 Jun 2020 21:56:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:56:37: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402769/SRX5402769.20_summits.bed INFO @ Mon, 29 Jun 2020 21:56:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling