Job ID = 6366308 SRX = SRX1078732 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:34:21 prefetch.2.10.7: 1) Downloading 'SRR2084339'... 2020-06-15T22:34:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:37:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:37:24 prefetch.2.10.7: 1) 'SRR2084339' was downloaded successfully Read 36216640 spots for SRR2084339/SRR2084339.sra Written 36216640 spots for SRR2084339/SRR2084339.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: 00:08:53 36216640 reads; of these: 36216640 (100.00%) were unpaired; of these: 429950 (1.19%) aligned 0 times 30083001 (83.06%) aligned exactly 1 time 5703689 (15.75%) aligned >1 times 98.81% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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 16 files... [bam_rmdupse_core] 8491756 / 35786690 = 0.2373 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 07:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.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 07:57:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:26: 1000000 INFO @ Tue, 16 Jun 2020 07:57:32: 2000000 INFO @ Tue, 16 Jun 2020 07:57:37: 3000000 INFO @ Tue, 16 Jun 2020 07:57:43: 4000000 INFO @ Tue, 16 Jun 2020 07:57:48: 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 07:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.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 07:57:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:54: 6000000 INFO @ Tue, 16 Jun 2020 07:57:56: 1000000 INFO @ Tue, 16 Jun 2020 07:57:59: 7000000 INFO @ Tue, 16 Jun 2020 07:58:02: 2000000 INFO @ Tue, 16 Jun 2020 07:58:05: 8000000 INFO @ Tue, 16 Jun 2020 07:58:08: 3000000 INFO @ Tue, 16 Jun 2020 07:58:11: 9000000 INFO @ Tue, 16 Jun 2020 07:58:14: 4000000 INFO @ Tue, 16 Jun 2020 07:58:17: 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 07:58:19: 5000000 INFO @ Tue, 16 Jun 2020 07:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.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 07:58:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:22: 11000000 INFO @ Tue, 16 Jun 2020 07:58:25: 6000000 INFO @ Tue, 16 Jun 2020 07:58:26: 1000000 INFO @ Tue, 16 Jun 2020 07:58:28: 12000000 INFO @ Tue, 16 Jun 2020 07:58:31: 7000000 INFO @ Tue, 16 Jun 2020 07:58:32: 2000000 INFO @ Tue, 16 Jun 2020 07:58:34: 13000000 INFO @ Tue, 16 Jun 2020 07:58:37: 8000000 INFO @ Tue, 16 Jun 2020 07:58:38: 3000000 INFO @ Tue, 16 Jun 2020 07:58:40: 14000000 INFO @ Tue, 16 Jun 2020 07:58:43: 9000000 INFO @ Tue, 16 Jun 2020 07:58:44: 4000000 INFO @ Tue, 16 Jun 2020 07:58:46: 15000000 INFO @ Tue, 16 Jun 2020 07:58:49: 10000000 INFO @ Tue, 16 Jun 2020 07:58:50: 5000000 INFO @ Tue, 16 Jun 2020 07:58:52: 16000000 INFO @ Tue, 16 Jun 2020 07:58:55: 11000000 INFO @ Tue, 16 Jun 2020 07:58:56: 6000000 INFO @ Tue, 16 Jun 2020 07:58:58: 17000000 INFO @ Tue, 16 Jun 2020 07:59:01: 12000000 INFO @ Tue, 16 Jun 2020 07:59:01: 7000000 INFO @ Tue, 16 Jun 2020 07:59:03: 18000000 INFO @ Tue, 16 Jun 2020 07:59:07: 13000000 INFO @ Tue, 16 Jun 2020 07:59:07: 8000000 INFO @ Tue, 16 Jun 2020 07:59:09: 19000000 INFO @ Tue, 16 Jun 2020 07:59:13: 9000000 INFO @ Tue, 16 Jun 2020 07:59:13: 14000000 INFO @ Tue, 16 Jun 2020 07:59:15: 20000000 INFO @ Tue, 16 Jun 2020 07:59:18: 10000000 INFO @ Tue, 16 Jun 2020 07:59:19: 15000000 INFO @ Tue, 16 Jun 2020 07:59:21: 21000000 INFO @ Tue, 16 Jun 2020 07:59:24: 11000000 INFO @ Tue, 16 Jun 2020 07:59:25: 16000000 INFO @ Tue, 16 Jun 2020 07:59:26: 22000000 INFO @ Tue, 16 Jun 2020 07:59:30: 12000000 INFO @ Tue, 16 Jun 2020 07:59:30: 17000000 INFO @ Tue, 16 Jun 2020 07:59:32: 23000000 INFO @ Tue, 16 Jun 2020 07:59:36: 13000000 INFO @ Tue, 16 Jun 2020 07:59:36: 18000000 INFO @ Tue, 16 Jun 2020 07:59:38: 24000000 INFO @ Tue, 16 Jun 2020 07:59:41: 14000000 INFO @ Tue, 16 Jun 2020 07:59:42: 19000000 INFO @ Tue, 16 Jun 2020 07:59:43: 25000000 INFO @ Tue, 16 Jun 2020 07:59:47: 15000000 INFO @ Tue, 16 Jun 2020 07:59:48: 20000000 INFO @ Tue, 16 Jun 2020 07:59:49: 26000000 INFO @ Tue, 16 Jun 2020 07:59:53: 16000000 INFO @ Tue, 16 Jun 2020 07:59:53: 21000000 INFO @ Tue, 16 Jun 2020 07:59:55: 27000000 INFO @ Tue, 16 Jun 2020 07:59:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:57: #1 total tags in treatment: 27294934 INFO @ Tue, 16 Jun 2020 07:59:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:57: #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 07:59:57: #1 tags after filtering in treatment: 27294934 INFO @ Tue, 16 Jun 2020 07:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:58: 17000000 INFO @ Tue, 16 Jun 2020 07:59:59: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 07:59:59: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:59: 22000000 INFO @ Tue, 16 Jun 2020 07:59:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:59:59: #2 alternative fragment length(s) may be 1,12,49,130,148,208,224,282,430,451,465,533 bps INFO @ Tue, 16 Jun 2020 07:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.05_model.r WARNING @ Tue, 16 Jun 2020 07:59:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:59: #2 You may need to consider one of the other alternative d(s): 1,12,49,130,148,208,224,282,430,451,465,533 WARNING @ Tue, 16 Jun 2020 07:59:59: #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 07:59:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:04: 18000000 INFO @ Tue, 16 Jun 2020 08:00:05: 23000000 INFO @ Tue, 16 Jun 2020 08:00:10: 19000000 INFO @ Tue, 16 Jun 2020 08:00:11: 24000000 INFO @ Tue, 16 Jun 2020 08:00:15: 20000000 INFO @ Tue, 16 Jun 2020 08:00:16: 25000000 INFO @ Tue, 16 Jun 2020 08:00:21: 21000000 INFO @ Tue, 16 Jun 2020 08:00:22: 26000000 INFO @ Tue, 16 Jun 2020 08:00:26: 22000000 INFO @ Tue, 16 Jun 2020 08:00:27: 27000000 INFO @ Tue, 16 Jun 2020 08:00:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:29: #1 total tags in treatment: 27294934 INFO @ Tue, 16 Jun 2020 08:00:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:29: #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 08:00:30: #1 tags after filtering in treatment: 27294934 INFO @ Tue, 16 Jun 2020 08:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:32: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 08:00:32: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:32: 23000000 INFO @ Tue, 16 Jun 2020 08:00:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:32: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:00:32: #2 alternative fragment length(s) may be 1,12,49,130,148,208,224,282,430,451,465,533 bps INFO @ Tue, 16 Jun 2020 08:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.10_model.r WARNING @ Tue, 16 Jun 2020 08:00:32: #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 08:00:32: #2 You may need to consider one of the other alternative d(s): 1,12,49,130,148,208,224,282,430,451,465,533 WARNING @ Tue, 16 Jun 2020 08:00:32: #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 08:00:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:37: 24000000 INFO @ Tue, 16 Jun 2020 08:00:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:43: 25000000 INFO @ Tue, 16 Jun 2020 08:00:48: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:54: 27000000 INFO @ Tue, 16 Jun 2020 08:00:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:55: #1 total tags in treatment: 27294934 INFO @ Tue, 16 Jun 2020 08:00:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:55: #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 08:00:56: #1 tags after filtering in treatment: 27294934 INFO @ Tue, 16 Jun 2020 08:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:58: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 08:00:58: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:58: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:00:58: #2 alternative fragment length(s) may be 1,12,49,130,148,208,224,282,430,451,465,533 bps INFO @ Tue, 16 Jun 2020 08:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.20_model.r WARNING @ Tue, 16 Jun 2020 08:00:58: #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 08:00:58: #2 You may need to consider one of the other alternative d(s): 1,12,49,130,148,208,224,282,430,451,465,533 WARNING @ Tue, 16 Jun 2020 08:00:58: #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 08:00:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.05_summits.bed INFO @ Tue, 16 Jun 2020 08:00:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078732/SRX1078732.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling