Job ID = 6367247 SRX = SRX3104610 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:16 prefetch.2.10.7: 1) Downloading 'SRR5946215'... 2020-06-15T23:17:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:29 prefetch.2.10.7: 'SRR5946215' is valid 2020-06-15T23:18:29 prefetch.2.10.7: 1) 'SRR5946215' was downloaded successfully 2020-06-15T23:18:29 prefetch.2.10.7: 'SRR5946215' has 0 unresolved dependencies Read 29453149 spots for SRR5946215/SRR5946215.sra Written 29453149 spots for SRR5946215/SRR5946215.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: 00:06:51 29453149 reads; of these: 29453149 (100.00%) were unpaired; of these: 612769 (2.08%) aligned 0 times 24066735 (81.71%) aligned exactly 1 time 4773645 (16.21%) aligned >1 times 97.92% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 3394584 / 28840380 = 0.1177 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 08:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.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 08:32:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:21: 1000000 INFO @ Tue, 16 Jun 2020 08:32:26: 2000000 INFO @ Tue, 16 Jun 2020 08:32:32: 3000000 INFO @ Tue, 16 Jun 2020 08:32:37: 4000000 INFO @ Tue, 16 Jun 2020 08:32:43: 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 08:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.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 08:32:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:48: 6000000 INFO @ Tue, 16 Jun 2020 08:32:52: 1000000 INFO @ Tue, 16 Jun 2020 08:32:54: 7000000 INFO @ Tue, 16 Jun 2020 08:32:59: 2000000 INFO @ Tue, 16 Jun 2020 08:33:00: 8000000 INFO @ Tue, 16 Jun 2020 08:33:06: 3000000 INFO @ Tue, 16 Jun 2020 08:33:06: 9000000 INFO @ Tue, 16 Jun 2020 08:33:12: 10000000 INFO @ Tue, 16 Jun 2020 08:33:12: 4000000 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 08:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.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 08:33:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:18: 11000000 INFO @ Tue, 16 Jun 2020 08:33:19: 5000000 INFO @ Tue, 16 Jun 2020 08:33:22: 1000000 INFO @ Tue, 16 Jun 2020 08:33:25: 12000000 INFO @ Tue, 16 Jun 2020 08:33:26: 6000000 INFO @ Tue, 16 Jun 2020 08:33:29: 2000000 INFO @ Tue, 16 Jun 2020 08:33:31: 13000000 INFO @ Tue, 16 Jun 2020 08:33:32: 7000000 INFO @ Tue, 16 Jun 2020 08:33:35: 3000000 INFO @ Tue, 16 Jun 2020 08:33:37: 14000000 INFO @ Tue, 16 Jun 2020 08:33:40: 8000000 INFO @ Tue, 16 Jun 2020 08:33:41: 4000000 INFO @ Tue, 16 Jun 2020 08:33:43: 15000000 INFO @ Tue, 16 Jun 2020 08:33:47: 9000000 INFO @ Tue, 16 Jun 2020 08:33:47: 5000000 INFO @ Tue, 16 Jun 2020 08:33:49: 16000000 INFO @ Tue, 16 Jun 2020 08:33:53: 6000000 INFO @ Tue, 16 Jun 2020 08:33:54: 10000000 INFO @ Tue, 16 Jun 2020 08:33:56: 17000000 INFO @ Tue, 16 Jun 2020 08:33:59: 7000000 INFO @ Tue, 16 Jun 2020 08:34:01: 11000000 INFO @ Tue, 16 Jun 2020 08:34:02: 18000000 INFO @ Tue, 16 Jun 2020 08:34:06: 8000000 INFO @ Tue, 16 Jun 2020 08:34:08: 19000000 INFO @ Tue, 16 Jun 2020 08:34:08: 12000000 INFO @ Tue, 16 Jun 2020 08:34:12: 9000000 INFO @ Tue, 16 Jun 2020 08:34:14: 20000000 INFO @ Tue, 16 Jun 2020 08:34:16: 13000000 INFO @ Tue, 16 Jun 2020 08:34:19: 10000000 INFO @ Tue, 16 Jun 2020 08:34:21: 21000000 INFO @ Tue, 16 Jun 2020 08:34:23: 14000000 INFO @ Tue, 16 Jun 2020 08:34:25: 11000000 INFO @ Tue, 16 Jun 2020 08:34:27: 22000000 INFO @ Tue, 16 Jun 2020 08:34:30: 15000000 INFO @ Tue, 16 Jun 2020 08:34:31: 12000000 INFO @ Tue, 16 Jun 2020 08:34:34: 23000000 INFO @ Tue, 16 Jun 2020 08:34:37: 16000000 INFO @ Tue, 16 Jun 2020 08:34:38: 13000000 INFO @ Tue, 16 Jun 2020 08:34:40: 24000000 INFO @ Tue, 16 Jun 2020 08:34:44: 14000000 INFO @ Tue, 16 Jun 2020 08:34:45: 17000000 INFO @ Tue, 16 Jun 2020 08:34:47: 25000000 INFO @ Tue, 16 Jun 2020 08:34:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:34:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:34:50: #1 total tags in treatment: 25445796 INFO @ Tue, 16 Jun 2020 08:34:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:50: #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 08:34:50: #1 tags after filtering in treatment: 25445796 INFO @ Tue, 16 Jun 2020 08:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:51: 15000000 INFO @ Tue, 16 Jun 2020 08:34:52: #2 number of paired peaks: 120 WARNING @ Tue, 16 Jun 2020 08:34:52: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:52: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:34:52: #2 alternative fragment length(s) may be 1,42,478,518,566 bps INFO @ Tue, 16 Jun 2020 08:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:52: #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 08:34:52: #2 You may need to consider one of the other alternative d(s): 1,42,478,518,566 WARNING @ Tue, 16 Jun 2020 08:34:52: #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 08:34:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:52: 18000000 INFO @ Tue, 16 Jun 2020 08:34:57: 16000000 INFO @ Tue, 16 Jun 2020 08:34:59: 19000000 INFO @ Tue, 16 Jun 2020 08:35:04: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:06: 20000000 INFO @ Tue, 16 Jun 2020 08:35:10: 18000000 INFO @ Tue, 16 Jun 2020 08:35:14: 21000000 INFO @ Tue, 16 Jun 2020 08:35:16: 19000000 INFO @ Tue, 16 Jun 2020 08:35:21: 22000000 INFO @ Tue, 16 Jun 2020 08:35:23: 20000000 INFO @ Tue, 16 Jun 2020 08:35:28: 23000000 INFO @ Tue, 16 Jun 2020 08:35:29: 21000000 INFO @ Tue, 16 Jun 2020 08:35:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:34: 24000000 INFO @ Tue, 16 Jun 2020 08:35:36: 22000000 INFO @ Tue, 16 Jun 2020 08:35:41: 25000000 INFO @ Tue, 16 Jun 2020 08:35:42: 23000000 INFO @ Tue, 16 Jun 2020 08:35:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:45: #1 total tags in treatment: 25445796 INFO @ Tue, 16 Jun 2020 08:35:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:45: #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 08:35:45: #1 tags after filtering in treatment: 25445796 INFO @ Tue, 16 Jun 2020 08:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:47: #2 number of paired peaks: 120 WARNING @ Tue, 16 Jun 2020 08:35:47: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:47: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:35:47: #2 alternative fragment length(s) may be 1,42,478,518,566 bps INFO @ Tue, 16 Jun 2020 08:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.10_model.r WARNING @ Tue, 16 Jun 2020 08:35:47: #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 08:35:47: #2 You may need to consider one of the other alternative d(s): 1,42,478,518,566 WARNING @ Tue, 16 Jun 2020 08:35:47: #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 08:35:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.05_summits.bed INFO @ Tue, 16 Jun 2020 08:35:47: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:48: 24000000 INFO @ Tue, 16 Jun 2020 08:35:54: 25000000 INFO @ Tue, 16 Jun 2020 08:35:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:56: #1 total tags in treatment: 25445796 INFO @ Tue, 16 Jun 2020 08:35:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:56: #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 08:35:57: #1 tags after filtering in treatment: 25445796 INFO @ Tue, 16 Jun 2020 08:35:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:59: #2 number of paired peaks: 120 WARNING @ Tue, 16 Jun 2020 08:35:59: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:35:59: #2 alternative fragment length(s) may be 1,42,478,518,566 bps INFO @ Tue, 16 Jun 2020 08:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:59: #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 08:35:59: #2 You may need to consider one of the other alternative d(s): 1,42,478,518,566 WARNING @ Tue, 16 Jun 2020 08:35:59: #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 08:35:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104610/SRX3104610.20_summits.bed INFO @ Tue, 16 Jun 2020 08:36:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling