Job ID = 6368672 SRX = SRX5402699 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:35 prefetch.2.10.7: 1) Downloading 'SRR8602933'... 2020-06-16T00:29:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:27 prefetch.2.10.7: 1) 'SRR8602933' was downloaded successfully Read 32338477 spots for SRR8602933/SRR8602933.sra Written 32338477 spots for SRR8602933/SRR8602933.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: 00:06:20 32338477 reads; of these: 32338477 (100.00%) were unpaired; of these: 8522871 (26.36%) aligned 0 times 17566201 (54.32%) aligned exactly 1 time 6249405 (19.32%) aligned >1 times 73.64% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 9065579 / 23815606 = 0.3807 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 09:45:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.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 09:45:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:25: 1000000 INFO @ Tue, 16 Jun 2020 09:45:30: 2000000 INFO @ Tue, 16 Jun 2020 09:45:35: 3000000 INFO @ Tue, 16 Jun 2020 09:45:40: 4000000 INFO @ Tue, 16 Jun 2020 09:45:46: 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 09:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.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 09:45:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:51: 6000000 INFO @ Tue, 16 Jun 2020 09:45:56: 7000000 INFO @ Tue, 16 Jun 2020 09:45:57: 1000000 INFO @ Tue, 16 Jun 2020 09:46:02: 8000000 INFO @ Tue, 16 Jun 2020 09:46:04: 2000000 INFO @ Tue, 16 Jun 2020 09:46:08: 9000000 INFO @ Tue, 16 Jun 2020 09:46:10: 3000000 INFO @ Tue, 16 Jun 2020 09:46:14: 10000000 INFO @ Tue, 16 Jun 2020 09:46:17: 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 09:46:19: 11000000 INFO @ Tue, 16 Jun 2020 09:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.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 09:46:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:24: 5000000 INFO @ Tue, 16 Jun 2020 09:46:25: 12000000 INFO @ Tue, 16 Jun 2020 09:46:26: 1000000 INFO @ Tue, 16 Jun 2020 09:46:31: 6000000 INFO @ Tue, 16 Jun 2020 09:46:31: 13000000 INFO @ Tue, 16 Jun 2020 09:46:32: 2000000 INFO @ Tue, 16 Jun 2020 09:46:37: 14000000 INFO @ Tue, 16 Jun 2020 09:46:37: 7000000 INFO @ Tue, 16 Jun 2020 09:46:38: 3000000 INFO @ Tue, 16 Jun 2020 09:46:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:41: #1 total tags in treatment: 14750027 INFO @ Tue, 16 Jun 2020 09:46:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:41: #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 09:46:41: #1 tags after filtering in treatment: 14750027 INFO @ Tue, 16 Jun 2020 09:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:42: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 09:46:42: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:42: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:46:42: #2 alternative fragment length(s) may be 1,29,45 bps INFO @ Tue, 16 Jun 2020 09:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.05_model.r WARNING @ Tue, 16 Jun 2020 09:46:42: #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 09:46:42: #2 You may need to consider one of the other alternative d(s): 1,29,45 WARNING @ Tue, 16 Jun 2020 09:46:42: #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 09:46:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:43: 4000000 INFO @ Tue, 16 Jun 2020 09:46:44: 8000000 INFO @ Tue, 16 Jun 2020 09:46:49: 5000000 INFO @ Tue, 16 Jun 2020 09:46:51: 9000000 INFO @ Tue, 16 Jun 2020 09:46:55: 6000000 INFO @ Tue, 16 Jun 2020 09:46:57: 10000000 INFO @ Tue, 16 Jun 2020 09:47:01: 7000000 INFO @ Tue, 16 Jun 2020 09:47:04: 11000000 INFO @ Tue, 16 Jun 2020 09:47:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:07: 8000000 INFO @ Tue, 16 Jun 2020 09:47:11: 12000000 INFO @ Tue, 16 Jun 2020 09:47:13: 9000000 INFO @ Tue, 16 Jun 2020 09:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:17: Done! INFO @ Tue, 16 Jun 2020 09:47:17: 13000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:18: 10000000 INFO @ Tue, 16 Jun 2020 09:47:24: 14000000 INFO @ Tue, 16 Jun 2020 09:47:24: 11000000 INFO @ Tue, 16 Jun 2020 09:47:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:29: #1 total tags in treatment: 14750027 INFO @ Tue, 16 Jun 2020 09:47:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:29: #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 09:47:29: #1 tags after filtering in treatment: 14750027 INFO @ Tue, 16 Jun 2020 09:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:30: 12000000 INFO @ Tue, 16 Jun 2020 09:47:30: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 09:47:30: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:30: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:30: #2 alternative fragment length(s) may be 1,29,45 bps INFO @ Tue, 16 Jun 2020 09:47:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.10_model.r WARNING @ Tue, 16 Jun 2020 09:47:30: #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 09:47:30: #2 You may need to consider one of the other alternative d(s): 1,29,45 WARNING @ Tue, 16 Jun 2020 09:47:30: #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 09:47:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:35: 13000000 INFO @ Tue, 16 Jun 2020 09:47:40: 14000000 INFO @ Tue, 16 Jun 2020 09:47:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:44: #1 total tags in treatment: 14750027 INFO @ Tue, 16 Jun 2020 09:47:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:44: #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 09:47:44: #1 tags after filtering in treatment: 14750027 INFO @ Tue, 16 Jun 2020 09:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:45: #2 number of paired peaks: 497 WARNING @ Tue, 16 Jun 2020 09:47:45: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:46: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:46: #2 alternative fragment length(s) may be 1,29,45 bps INFO @ Tue, 16 Jun 2020 09:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.20_model.r WARNING @ Tue, 16 Jun 2020 09:47:46: #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 09:47:46: #2 You may need to consider one of the other alternative d(s): 1,29,45 WARNING @ Tue, 16 Jun 2020 09:47:46: #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 09:47:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.10_summits.bed INFO @ Tue, 16 Jun 2020 09:48:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402699/SRX5402699.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling