Job ID = 6367652 SRX = SRX373274 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:20 prefetch.2.10.7: 1) Downloading 'SRR1024192'... 2020-06-15T23:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:21 prefetch.2.10.7: 1) 'SRR1024192' was downloaded successfully Read 30925633 spots for SRR1024192/SRR1024192.sra Written 30925633 spots for SRR1024192/SRR1024192.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: 00:05:29 30925633 reads; of these: 30925633 (100.00%) were unpaired; of these: 10862193 (35.12%) aligned 0 times 16576591 (53.60%) aligned exactly 1 time 3486849 (11.27%) aligned >1 times 64.88% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 2309509 / 20063440 = 0.1151 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 08:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.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 08:52:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:39: 1000000 INFO @ Tue, 16 Jun 2020 08:52:46: 2000000 INFO @ Tue, 16 Jun 2020 08:52:53: 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 @ Tue, 16 Jun 2020 08:53:01: 4000000 INFO @ Tue, 16 Jun 2020 08:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.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 08:53:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:08: 5000000 INFO @ Tue, 16 Jun 2020 08:53:10: 1000000 INFO @ Tue, 16 Jun 2020 08:53:16: 6000000 INFO @ Tue, 16 Jun 2020 08:53:18: 2000000 INFO @ Tue, 16 Jun 2020 08:53:24: 7000000 INFO @ Tue, 16 Jun 2020 08:53:26: 3000000 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 08:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.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 08:53:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:32: 8000000 INFO @ Tue, 16 Jun 2020 08:53:34: 4000000 INFO @ Tue, 16 Jun 2020 08:53:40: 1000000 INFO @ Tue, 16 Jun 2020 08:53:41: 9000000 INFO @ Tue, 16 Jun 2020 08:53:42: 5000000 INFO @ Tue, 16 Jun 2020 08:53:48: 2000000 INFO @ Tue, 16 Jun 2020 08:53:49: 10000000 INFO @ Tue, 16 Jun 2020 08:53:50: 6000000 INFO @ Tue, 16 Jun 2020 08:53:57: 3000000 INFO @ Tue, 16 Jun 2020 08:53:57: 11000000 INFO @ Tue, 16 Jun 2020 08:53:59: 7000000 INFO @ Tue, 16 Jun 2020 08:54:05: 4000000 INFO @ Tue, 16 Jun 2020 08:54:06: 12000000 INFO @ Tue, 16 Jun 2020 08:54:07: 8000000 INFO @ Tue, 16 Jun 2020 08:54:13: 5000000 INFO @ Tue, 16 Jun 2020 08:54:14: 13000000 INFO @ Tue, 16 Jun 2020 08:54:15: 9000000 INFO @ Tue, 16 Jun 2020 08:54:21: 6000000 INFO @ Tue, 16 Jun 2020 08:54:23: 14000000 INFO @ Tue, 16 Jun 2020 08:54:23: 10000000 INFO @ Tue, 16 Jun 2020 08:54:29: 7000000 INFO @ Tue, 16 Jun 2020 08:54:31: 15000000 INFO @ Tue, 16 Jun 2020 08:54:31: 11000000 INFO @ Tue, 16 Jun 2020 08:54:37: 8000000 INFO @ Tue, 16 Jun 2020 08:54:39: 16000000 INFO @ Tue, 16 Jun 2020 08:54:40: 12000000 INFO @ Tue, 16 Jun 2020 08:54:46: 9000000 INFO @ Tue, 16 Jun 2020 08:54:47: 17000000 INFO @ Tue, 16 Jun 2020 08:54:48: 13000000 INFO @ Tue, 16 Jun 2020 08:54:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:54:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:54:53: #1 total tags in treatment: 17753931 INFO @ Tue, 16 Jun 2020 08:54:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:53: #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 08:54:54: #1 tags after filtering in treatment: 17753931 INFO @ Tue, 16 Jun 2020 08:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:54:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:54: 10000000 INFO @ Tue, 16 Jun 2020 08:54:55: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:54:55: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:55: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:54:55: #2 alternative fragment length(s) may be 1,21,521,548,578,598 bps INFO @ Tue, 16 Jun 2020 08:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.05_model.r WARNING @ Tue, 16 Jun 2020 08:54:55: #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 08:54:55: #2 You may need to consider one of the other alternative d(s): 1,21,521,548,578,598 WARNING @ Tue, 16 Jun 2020 08:54:55: #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 08:54:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:56: 14000000 INFO @ Tue, 16 Jun 2020 08:55:02: 11000000 INFO @ Tue, 16 Jun 2020 08:55:04: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:55:10: 12000000 INFO @ Tue, 16 Jun 2020 08:55:12: 16000000 INFO @ Tue, 16 Jun 2020 08:55:18: 13000000 INFO @ Tue, 16 Jun 2020 08:55:20: 17000000 INFO @ Tue, 16 Jun 2020 08:55:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:55:26: 14000000 INFO @ Tue, 16 Jun 2020 08:55:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:55:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:55:26: #1 total tags in treatment: 17753931 INFO @ Tue, 16 Jun 2020 08:55:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:26: #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 08:55:26: #1 tags after filtering in treatment: 17753931 INFO @ Tue, 16 Jun 2020 08:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:27: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:55:27: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:27: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:55:27: #2 alternative fragment length(s) may be 1,21,521,548,578,598 bps INFO @ Tue, 16 Jun 2020 08:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.10_model.r WARNING @ Tue, 16 Jun 2020 08:55:27: #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 08:55:27: #2 You may need to consider one of the other alternative d(s): 1,21,521,548,578,598 WARNING @ Tue, 16 Jun 2020 08:55:27: #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 08:55:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:33: 15000000 INFO @ Tue, 16 Jun 2020 08:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.05_summits.bed INFO @ Tue, 16 Jun 2020 08:55:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:55:40: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:47: 17000000 INFO @ Tue, 16 Jun 2020 08:55:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:55:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:55:53: #1 total tags in treatment: 17753931 INFO @ Tue, 16 Jun 2020 08:55:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:53: #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 08:55:53: #1 tags after filtering in treatment: 17753931 INFO @ Tue, 16 Jun 2020 08:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:54: #2 number of paired peaks: 229 WARNING @ Tue, 16 Jun 2020 08:55:54: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:55:54: #2 alternative fragment length(s) may be 1,21,521,548,578,598 bps INFO @ Tue, 16 Jun 2020 08:55:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.20_model.r WARNING @ Tue, 16 Jun 2020 08:55:55: #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 08:55:55: #2 You may need to consider one of the other alternative d(s): 1,21,521,548,578,598 WARNING @ Tue, 16 Jun 2020 08:55:55: #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 08:55:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.10_summits.bed INFO @ Tue, 16 Jun 2020 08:56:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373274/SRX373274.20_summits.bed INFO @ Tue, 16 Jun 2020 08:56:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling