Job ID = 6368053 SRX = SRX466516 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:54 prefetch.2.10.7: 1) Downloading 'SRR1163582'... 2020-06-16T00:06:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:33 prefetch.2.10.7: 1) 'SRR1163582' was downloaded successfully Read 21509609 spots for SRR1163582/SRR1163582.sra Written 21509609 spots for SRR1163582/SRR1163582.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: 00:04:06 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255410 (1.19%) aligned 0 times 17821452 (82.85%) aligned exactly 1 time 3432747 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 3667698 / 21254199 = 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 09:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.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 09:22:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:58: 1000000 INFO @ Tue, 16 Jun 2020 09:23:03: 2000000 INFO @ Tue, 16 Jun 2020 09:23:08: 3000000 INFO @ Tue, 16 Jun 2020 09:23:12: 4000000 INFO @ Tue, 16 Jun 2020 09:23:17: 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 09:23:22: 6000000 INFO @ Tue, 16 Jun 2020 09:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.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 09:23:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:27: 7000000 INFO @ Tue, 16 Jun 2020 09:23:28: 1000000 INFO @ Tue, 16 Jun 2020 09:23:32: 8000000 INFO @ Tue, 16 Jun 2020 09:23:33: 2000000 INFO @ Tue, 16 Jun 2020 09:23:36: 9000000 INFO @ Tue, 16 Jun 2020 09:23:38: 3000000 INFO @ Tue, 16 Jun 2020 09:23:41: 10000000 INFO @ Tue, 16 Jun 2020 09:23:43: 4000000 INFO @ Tue, 16 Jun 2020 09:23:46: 11000000 INFO @ Tue, 16 Jun 2020 09:23:48: 5000000 INFO @ Tue, 16 Jun 2020 09:23:51: 12000000 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 09:23:53: 6000000 INFO @ Tue, 16 Jun 2020 09:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.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 09:23:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:56: 13000000 INFO @ Tue, 16 Jun 2020 09:23:58: 7000000 INFO @ Tue, 16 Jun 2020 09:23:59: 1000000 INFO @ Tue, 16 Jun 2020 09:24:01: 14000000 INFO @ Tue, 16 Jun 2020 09:24:03: 8000000 INFO @ Tue, 16 Jun 2020 09:24:04: 2000000 INFO @ Tue, 16 Jun 2020 09:24:06: 15000000 INFO @ Tue, 16 Jun 2020 09:24:08: 9000000 INFO @ Tue, 16 Jun 2020 09:24:10: 3000000 INFO @ Tue, 16 Jun 2020 09:24:12: 16000000 INFO @ Tue, 16 Jun 2020 09:24:13: 10000000 INFO @ Tue, 16 Jun 2020 09:24:16: 4000000 INFO @ Tue, 16 Jun 2020 09:24:17: 17000000 INFO @ Tue, 16 Jun 2020 09:24:18: 11000000 INFO @ Tue, 16 Jun 2020 09:24:20: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:24:20: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:24:20: #1 total tags in treatment: 17586501 INFO @ Tue, 16 Jun 2020 09:24:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:20: #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 09:24:20: #1 tags after filtering in treatment: 17586501 INFO @ Tue, 16 Jun 2020 09:24:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:21: 5000000 INFO @ Tue, 16 Jun 2020 09:24:21: #2 number of paired peaks: 206 WARNING @ Tue, 16 Jun 2020 09:24:21: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:24:22: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 16 Jun 2020 09:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:22: #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 09:24:22: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 16 Jun 2020 09:24:22: #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 09:24:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:23: 12000000 INFO @ Tue, 16 Jun 2020 09:24:27: 6000000 INFO @ Tue, 16 Jun 2020 09:24:28: 13000000 INFO @ Tue, 16 Jun 2020 09:24:32: 7000000 INFO @ Tue, 16 Jun 2020 09:24:33: 14000000 INFO @ Tue, 16 Jun 2020 09:24:38: 8000000 INFO @ Tue, 16 Jun 2020 09:24:38: 15000000 INFO @ Tue, 16 Jun 2020 09:24:43: 9000000 INFO @ Tue, 16 Jun 2020 09:24:43: 16000000 INFO @ Tue, 16 Jun 2020 09:24:49: 17000000 INFO @ Tue, 16 Jun 2020 09:24:49: 10000000 INFO @ Tue, 16 Jun 2020 09:24:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:24:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:24:52: #1 total tags in treatment: 17586501 INFO @ Tue, 16 Jun 2020 09:24:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:52: #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 09:24:52: #1 tags after filtering in treatment: 17586501 INFO @ Tue, 16 Jun 2020 09:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:53: #2 number of paired peaks: 206 WARNING @ Tue, 16 Jun 2020 09:24:53: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:53: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:24:53: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 16 Jun 2020 09:24:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.10_model.r WARNING @ Tue, 16 Jun 2020 09:24:53: #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 09:24:53: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 16 Jun 2020 09:24:53: #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 09:24:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:55: 11000000 INFO @ Tue, 16 Jun 2020 09:25:01: 12000000 INFO @ Tue, 16 Jun 2020 09:25:06: 13000000 INFO @ Tue, 16 Jun 2020 09:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:12: 14000000 INFO @ Tue, 16 Jun 2020 09:25:17: 15000000 INFO @ Tue, 16 Jun 2020 09:25:23: 16000000 INFO @ Tue, 16 Jun 2020 09:25:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:29: 17000000 INFO @ Tue, 16 Jun 2020 09:25:32: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:25:32: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:25:32: #1 total tags in treatment: 17586501 INFO @ Tue, 16 Jun 2020 09:25:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:32: #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 09:25:33: #1 tags after filtering in treatment: 17586501 INFO @ Tue, 16 Jun 2020 09:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:34: #2 number of paired peaks: 206 WARNING @ Tue, 16 Jun 2020 09:25:34: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:34: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:25:34: #2 alternative fragment length(s) may be 1,39 bps INFO @ Tue, 16 Jun 2020 09:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.20_model.r WARNING @ Tue, 16 Jun 2020 09:25:34: #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 09:25:34: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Tue, 16 Jun 2020 09:25:34: #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 09:25:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.10_summits.bed INFO @ Tue, 16 Jun 2020 09:25:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466516/SRX466516.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling