Job ID = 6368073 SRX = SRX466536 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:02:30 prefetch.2.10.7: 1) Downloading 'SRR1163602'... 2020-06-16T00:02:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:17 prefetch.2.10.7: 1) 'SRR1163602' was downloaded successfully Read 21509609 spots for SRR1163602/SRR1163602.sra Written 21509609 spots for SRR1163602/SRR1163602.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: 00:04:08 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255405 (1.19%) aligned 0 times 17821466 (82.85%) aligned exactly 1 time 3432738 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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 8 files... [bam_rmdupse_core] 3667825 / 21254204 = 0.1726 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 09:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.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 09:16:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:00: 1000000 INFO @ Tue, 16 Jun 2020 09:17:05: 2000000 INFO @ Tue, 16 Jun 2020 09:17:10: 3000000 INFO @ Tue, 16 Jun 2020 09:17:15: 4000000 INFO @ Tue, 16 Jun 2020 09:17:20: 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 09:17:25: 6000000 INFO @ Tue, 16 Jun 2020 09:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.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 09:17:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:30: 7000000 INFO @ Tue, 16 Jun 2020 09:17:30: 1000000 INFO @ Tue, 16 Jun 2020 09:17:35: 8000000 INFO @ Tue, 16 Jun 2020 09:17:35: 2000000 INFO @ Tue, 16 Jun 2020 09:17:40: 9000000 INFO @ Tue, 16 Jun 2020 09:17:40: 3000000 INFO @ Tue, 16 Jun 2020 09:17:45: 4000000 INFO @ Tue, 16 Jun 2020 09:17:45: 10000000 INFO @ Tue, 16 Jun 2020 09:17:50: 5000000 INFO @ Tue, 16 Jun 2020 09:17:50: 11000000 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 09:17:55: 6000000 INFO @ Tue, 16 Jun 2020 09:17:55: 12000000 INFO @ Tue, 16 Jun 2020 09:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.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 09:17:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:00: 7000000 INFO @ Tue, 16 Jun 2020 09:18:00: 13000000 INFO @ Tue, 16 Jun 2020 09:18:04: 1000000 INFO @ Tue, 16 Jun 2020 09:18:05: 8000000 INFO @ Tue, 16 Jun 2020 09:18:05: 14000000 INFO @ Tue, 16 Jun 2020 09:18:09: 2000000 INFO @ Tue, 16 Jun 2020 09:18:09: 9000000 INFO @ Tue, 16 Jun 2020 09:18:10: 15000000 INFO @ Tue, 16 Jun 2020 09:18:14: 3000000 INFO @ Tue, 16 Jun 2020 09:18:14: 10000000 INFO @ Tue, 16 Jun 2020 09:18:14: 16000000 INFO @ Tue, 16 Jun 2020 09:18:18: 4000000 INFO @ Tue, 16 Jun 2020 09:18:19: 11000000 INFO @ Tue, 16 Jun 2020 09:18:19: 17000000 INFO @ Tue, 16 Jun 2020 09:18:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:18:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:18:22: #1 total tags in treatment: 17586379 INFO @ Tue, 16 Jun 2020 09:18:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:22: #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 09:18:22: #1 tags after filtering in treatment: 17586379 INFO @ Tue, 16 Jun 2020 09:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:23: 5000000 INFO @ Tue, 16 Jun 2020 09:18:23: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:18:23: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:18:24: #2 alternative fragment length(s) may be 1,45,543 bps INFO @ Tue, 16 Jun 2020 09:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.05_model.r WARNING @ Tue, 16 Jun 2020 09:18:24: #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 09:18:24: #2 You may need to consider one of the other alternative d(s): 1,45,543 WARNING @ Tue, 16 Jun 2020 09:18:24: #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 09:18:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:24: 12000000 INFO @ Tue, 16 Jun 2020 09:18:28: 6000000 INFO @ Tue, 16 Jun 2020 09:18:28: 13000000 INFO @ Tue, 16 Jun 2020 09:18:33: 7000000 INFO @ Tue, 16 Jun 2020 09:18:33: 14000000 INFO @ Tue, 16 Jun 2020 09:18:37: 8000000 INFO @ Tue, 16 Jun 2020 09:18:38: 15000000 INFO @ Tue, 16 Jun 2020 09:18:42: 9000000 INFO @ Tue, 16 Jun 2020 09:18:42: 16000000 INFO @ Tue, 16 Jun 2020 09:18:47: 17000000 INFO @ Tue, 16 Jun 2020 09:18:47: 10000000 INFO @ Tue, 16 Jun 2020 09:18:50: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:18:50: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:18:50: #1 total tags in treatment: 17586379 INFO @ Tue, 16 Jun 2020 09:18:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:50: #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 09:18:50: #1 tags after filtering in treatment: 17586379 INFO @ Tue, 16 Jun 2020 09:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:51: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:18:51: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:51: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:18:51: #2 alternative fragment length(s) may be 1,45,543 bps INFO @ Tue, 16 Jun 2020 09:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.10_model.r WARNING @ Tue, 16 Jun 2020 09:18:51: #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 09:18:51: #2 You may need to consider one of the other alternative d(s): 1,45,543 WARNING @ Tue, 16 Jun 2020 09:18:51: #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 09:18:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:52: 11000000 INFO @ Tue, 16 Jun 2020 09:18:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:56: 12000000 INFO @ Tue, 16 Jun 2020 09:19:01: 13000000 INFO @ Tue, 16 Jun 2020 09:19:06: 14000000 INFO @ Tue, 16 Jun 2020 09:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:10: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:19:15: 16000000 INFO @ Tue, 16 Jun 2020 09:19:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:20: 17000000 INFO @ Tue, 16 Jun 2020 09:19:23: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:23: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:23: #1 total tags in treatment: 17586379 INFO @ Tue, 16 Jun 2020 09:19:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:23: #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 09:19:23: #1 tags after filtering in treatment: 17586379 INFO @ Tue, 16 Jun 2020 09:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:24: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:19:24: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:19:24: #2 alternative fragment length(s) may be 1,45,543 bps INFO @ Tue, 16 Jun 2020 09:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.20_model.r WARNING @ Tue, 16 Jun 2020 09:19:24: #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 09:19:24: #2 You may need to consider one of the other alternative d(s): 1,45,543 WARNING @ Tue, 16 Jun 2020 09:19:24: #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 09:19:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.10_summits.bed INFO @ Tue, 16 Jun 2020 09:19:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466536/SRX466536.20_summits.bed INFO @ Tue, 16 Jun 2020 09:20:07: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling