Job ID = 6527405 SRX = SRX2973385 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:17:54 prefetch.2.10.7: 1) Downloading 'SRR5786984'... 2020-06-29T12:17:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:21:18 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:21:18 prefetch.2.10.7: 1) 'SRR5786984' was downloaded successfully 2020-06-29T12:21:18 prefetch.2.10.7: 'SRR5786984' has 0 unresolved dependencies Read 45844906 spots for SRR5786984/SRR5786984.sra Written 45844906 spots for SRR5786984/SRR5786984.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: 00:15:15 45844906 reads; of these: 45844906 (100.00%) were unpaired; of these: 5563080 (12.13%) aligned 0 times 33530481 (73.14%) aligned exactly 1 time 6751345 (14.73%) aligned >1 times 87.87% overall alignment rate Time searching: 00:15:16 Overall time: 00:15:16 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 20 files... [bam_rmdupse_core] 10513262 / 40281826 = 0.2610 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 22:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.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 22:04:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:04:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:04:43: 1000000 INFO @ Mon, 29 Jun 2020 22:04:50: 2000000 INFO @ Mon, 29 Jun 2020 22:04:57: 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 @ Mon, 29 Jun 2020 22:05:04: 4000000 INFO @ Mon, 29 Jun 2020 22:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.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 22:05:05: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:05:05: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:05:13: 5000000 INFO @ Mon, 29 Jun 2020 22:05:15: 1000000 INFO @ Mon, 29 Jun 2020 22:05:22: 6000000 INFO @ Mon, 29 Jun 2020 22:05:25: 2000000 INFO @ Mon, 29 Jun 2020 22:05:30: 7000000 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 22:05:34: 3000000 INFO @ Mon, 29 Jun 2020 22:05:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.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 22:05:35: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:05:35: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:05:39: 8000000 INFO @ Mon, 29 Jun 2020 22:05:44: 4000000 INFO @ Mon, 29 Jun 2020 22:05:44: 1000000 INFO @ Mon, 29 Jun 2020 22:05:48: 9000000 INFO @ Mon, 29 Jun 2020 22:05:53: 2000000 INFO @ Mon, 29 Jun 2020 22:05:54: 5000000 INFO @ Mon, 29 Jun 2020 22:05:57: 10000000 INFO @ Mon, 29 Jun 2020 22:06:02: 3000000 INFO @ Mon, 29 Jun 2020 22:06:04: 6000000 INFO @ Mon, 29 Jun 2020 22:06:06: 11000000 INFO @ Mon, 29 Jun 2020 22:06:11: 4000000 INFO @ Mon, 29 Jun 2020 22:06:15: 7000000 INFO @ Mon, 29 Jun 2020 22:06:15: 12000000 INFO @ Mon, 29 Jun 2020 22:06:20: 5000000 INFO @ Mon, 29 Jun 2020 22:06:24: 13000000 INFO @ Mon, 29 Jun 2020 22:06:25: 8000000 INFO @ Mon, 29 Jun 2020 22:06:29: 6000000 INFO @ Mon, 29 Jun 2020 22:06:33: 14000000 INFO @ Mon, 29 Jun 2020 22:06:35: 9000000 INFO @ Mon, 29 Jun 2020 22:06:38: 7000000 INFO @ Mon, 29 Jun 2020 22:06:42: 15000000 INFO @ Mon, 29 Jun 2020 22:06:45: 10000000 INFO @ Mon, 29 Jun 2020 22:06:46: 8000000 INFO @ Mon, 29 Jun 2020 22:06:51: 16000000 INFO @ Mon, 29 Jun 2020 22:06:55: 11000000 INFO @ Mon, 29 Jun 2020 22:06:55: 9000000 INFO @ Mon, 29 Jun 2020 22:07:00: 17000000 INFO @ Mon, 29 Jun 2020 22:07:04: 12000000 INFO @ Mon, 29 Jun 2020 22:07:04: 10000000 INFO @ Mon, 29 Jun 2020 22:07:09: 18000000 INFO @ Mon, 29 Jun 2020 22:07:13: 11000000 INFO @ Mon, 29 Jun 2020 22:07:14: 13000000 INFO @ Mon, 29 Jun 2020 22:07:18: 19000000 INFO @ Mon, 29 Jun 2020 22:07:22: 12000000 INFO @ Mon, 29 Jun 2020 22:07:24: 14000000 INFO @ Mon, 29 Jun 2020 22:07:27: 20000000 INFO @ Mon, 29 Jun 2020 22:07:31: 13000000 INFO @ Mon, 29 Jun 2020 22:07:34: 15000000 INFO @ Mon, 29 Jun 2020 22:07:36: 21000000 INFO @ Mon, 29 Jun 2020 22:07:40: 14000000 INFO @ Mon, 29 Jun 2020 22:07:44: 16000000 INFO @ Mon, 29 Jun 2020 22:07:45: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:07:49: 15000000 INFO @ Mon, 29 Jun 2020 22:07:54: 17000000 INFO @ Mon, 29 Jun 2020 22:07:54: 23000000 INFO @ Mon, 29 Jun 2020 22:07:58: 16000000 INFO @ Mon, 29 Jun 2020 22:08:03: 24000000 INFO @ Mon, 29 Jun 2020 22:08:04: 18000000 INFO @ Mon, 29 Jun 2020 22:08:07: 17000000 INFO @ Mon, 29 Jun 2020 22:08:13: 25000000 INFO @ Mon, 29 Jun 2020 22:08:13: 19000000 INFO @ Mon, 29 Jun 2020 22:08:16: 18000000 INFO @ Mon, 29 Jun 2020 22:08:22: 26000000 INFO @ Mon, 29 Jun 2020 22:08:23: 20000000 INFO @ Mon, 29 Jun 2020 22:08:25: 19000000 INFO @ Mon, 29 Jun 2020 22:08:31: 27000000 INFO @ Mon, 29 Jun 2020 22:08:33: 21000000 INFO @ Mon, 29 Jun 2020 22:08:34: 20000000 INFO @ Mon, 29 Jun 2020 22:08:40: 28000000 INFO @ Mon, 29 Jun 2020 22:08:43: 21000000 INFO @ Mon, 29 Jun 2020 22:08:43: 22000000 INFO @ Mon, 29 Jun 2020 22:08:49: 29000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:08:52: 22000000 INFO @ Mon, 29 Jun 2020 22:08:53: 23000000 INFO @ Mon, 29 Jun 2020 22:08:56: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:08:56: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:08:56: #1 total tags in treatment: 29768564 INFO @ Mon, 29 Jun 2020 22:08:56: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:08:56: #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 22:08:56: #1 tags after filtering in treatment: 29768564 INFO @ Mon, 29 Jun 2020 22:08:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:08:56: #1 finished! INFO @ Mon, 29 Jun 2020 22:08:56: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:08:58: #2 number of paired peaks: 100 WARNING @ Mon, 29 Jun 2020 22:08:58: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Mon, 29 Jun 2020 22:08:58: start model_add_line... INFO @ Mon, 29 Jun 2020 22:08:59: start X-correlation... INFO @ Mon, 29 Jun 2020 22:08:59: end of X-cor INFO @ Mon, 29 Jun 2020 22:08:59: #2 finished! INFO @ Mon, 29 Jun 2020 22:08:59: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:08:59: #2 alternative fragment length(s) may be 1,34,52,78,282,378,399,553 bps INFO @ Mon, 29 Jun 2020 22:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.05_model.r WARNING @ Mon, 29 Jun 2020 22:08:59: #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 22:08:59: #2 You may need to consider one of the other alternative d(s): 1,34,52,78,282,378,399,553 WARNING @ Mon, 29 Jun 2020 22:08:59: #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 22:08:59: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:08:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:09:01: 23000000 INFO @ Mon, 29 Jun 2020 22:09:03: 24000000 INFO @ Mon, 29 Jun 2020 22:09:10: 24000000 INFO @ Mon, 29 Jun 2020 22:09:12: 25000000 INFO @ Mon, 29 Jun 2020 22:09:19: 25000000 INFO @ Mon, 29 Jun 2020 22:09:22: 26000000 INFO @ Mon, 29 Jun 2020 22:09:27: 26000000 INFO @ Mon, 29 Jun 2020 22:09:31: 27000000 INFO @ Mon, 29 Jun 2020 22:09:36: 27000000 INFO @ Mon, 29 Jun 2020 22:09:41: 28000000 INFO @ Mon, 29 Jun 2020 22:09:42: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:09:45: 28000000 INFO @ Mon, 29 Jun 2020 22:09:51: 29000000 INFO @ Mon, 29 Jun 2020 22:09:54: 29000000 INFO @ Mon, 29 Jun 2020 22:09:59: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:09:59: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:09:59: #1 total tags in treatment: 29768564 INFO @ Mon, 29 Jun 2020 22:09:59: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:09:59: #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 22:09:59: #1 tags after filtering in treatment: 29768564 INFO @ Mon, 29 Jun 2020 22:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:09:59: #1 finished! INFO @ Mon, 29 Jun 2020 22:09:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:10:00: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:10:00: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:10:00: #1 total tags in treatment: 29768564 INFO @ Mon, 29 Jun 2020 22:10:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:10:00: #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 22:10:01: #1 tags after filtering in treatment: 29768564 INFO @ Mon, 29 Jun 2020 22:10:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:10:01: #1 finished! INFO @ Mon, 29 Jun 2020 22:10:01: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:10:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:10:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:10:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.05_summits.bed INFO @ Mon, 29 Jun 2020 22:10:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:10:01: #2 number of paired peaks: 100 WARNING @ Mon, 29 Jun 2020 22:10:01: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Mon, 29 Jun 2020 22:10:01: start model_add_line... INFO @ Mon, 29 Jun 2020 22:10:01: start X-correlation... INFO @ Mon, 29 Jun 2020 22:10:01: end of X-cor INFO @ Mon, 29 Jun 2020 22:10:01: #2 finished! INFO @ Mon, 29 Jun 2020 22:10:01: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:10:01: #2 alternative fragment length(s) may be 1,34,52,78,282,378,399,553 bps INFO @ Mon, 29 Jun 2020 22:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.10_model.r WARNING @ Mon, 29 Jun 2020 22:10:01: #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 22:10:01: #2 You may need to consider one of the other alternative d(s): 1,34,52,78,282,378,399,553 WARNING @ Mon, 29 Jun 2020 22:10:01: #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 22:10:01: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:10:03: #2 number of paired peaks: 100 WARNING @ Mon, 29 Jun 2020 22:10:03: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Mon, 29 Jun 2020 22:10:03: start model_add_line... INFO @ Mon, 29 Jun 2020 22:10:03: start X-correlation... INFO @ Mon, 29 Jun 2020 22:10:03: end of X-cor INFO @ Mon, 29 Jun 2020 22:10:03: #2 finished! INFO @ Mon, 29 Jun 2020 22:10:03: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:10:03: #2 alternative fragment length(s) may be 1,34,52,78,282,378,399,553 bps INFO @ Mon, 29 Jun 2020 22:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.20_model.r WARNING @ Mon, 29 Jun 2020 22:10:03: #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 22:10:03: #2 You may need to consider one of the other alternative d(s): 1,34,52,78,282,378,399,553 WARNING @ Mon, 29 Jun 2020 22:10:03: #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 22:10:03: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:10:43: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:10:44: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.20_summits.bed INFO @ Mon, 29 Jun 2020 22:11:02: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:11:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:11:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:11:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2973385/SRX2973385.10_summits.bed INFO @ Mon, 29 Jun 2020 22:11:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling