Job ID = 6368161 SRX = SRX494845 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:57:35 prefetch.2.10.7: 1) Downloading 'SRR1198377'... 2020-06-15T23:57:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:40 prefetch.2.10.7: 1) 'SRR1198377' was downloaded successfully Read 21509609 spots for SRR1198377/SRR1198377.sra Written 21509609 spots for SRR1198377/SRR1198377.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: 00:03:57 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255408 (1.19%) aligned 0 times 17821599 (82.85%) aligned exactly 1 time 3432602 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 3667093 / 21254201 = 0.1725 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 09:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.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 09:10:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:44: 1000000 INFO @ Tue, 16 Jun 2020 09:10:49: 2000000 INFO @ Tue, 16 Jun 2020 09:10:54: 3000000 INFO @ Tue, 16 Jun 2020 09:10:59: 4000000 INFO @ Tue, 16 Jun 2020 09:11:04: 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 09:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.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 09:11:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:09: 6000000 INFO @ Tue, 16 Jun 2020 09:11:14: 7000000 INFO @ Tue, 16 Jun 2020 09:11:15: 1000000 INFO @ Tue, 16 Jun 2020 09:11:19: 8000000 INFO @ Tue, 16 Jun 2020 09:11:20: 2000000 INFO @ Tue, 16 Jun 2020 09:11:25: 9000000 INFO @ Tue, 16 Jun 2020 09:11:25: 3000000 INFO @ Tue, 16 Jun 2020 09:11:30: 10000000 INFO @ Tue, 16 Jun 2020 09:11:30: 4000000 INFO @ Tue, 16 Jun 2020 09:11:35: 11000000 INFO @ Tue, 16 Jun 2020 09:11:35: 5000000 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 09:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.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 09:11:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:40: 12000000 INFO @ Tue, 16 Jun 2020 09:11:41: 6000000 INFO @ Tue, 16 Jun 2020 09:11:45: 1000000 INFO @ Tue, 16 Jun 2020 09:11:46: 13000000 INFO @ Tue, 16 Jun 2020 09:11:46: 7000000 INFO @ Tue, 16 Jun 2020 09:11:51: 2000000 INFO @ Tue, 16 Jun 2020 09:11:51: 8000000 INFO @ Tue, 16 Jun 2020 09:11:52: 14000000 INFO @ Tue, 16 Jun 2020 09:11:56: 3000000 INFO @ Tue, 16 Jun 2020 09:11:57: 9000000 INFO @ Tue, 16 Jun 2020 09:11:57: 15000000 INFO @ Tue, 16 Jun 2020 09:12:02: 4000000 INFO @ Tue, 16 Jun 2020 09:12:02: 10000000 INFO @ Tue, 16 Jun 2020 09:12:03: 16000000 INFO @ Tue, 16 Jun 2020 09:12:08: 5000000 INFO @ Tue, 16 Jun 2020 09:12:08: 11000000 INFO @ Tue, 16 Jun 2020 09:12:09: 17000000 INFO @ Tue, 16 Jun 2020 09:12:12: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:12: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:12: #1 total tags in treatment: 17587108 INFO @ Tue, 16 Jun 2020 09:12:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:12: #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 09:12:12: #1 tags after filtering in treatment: 17587108 INFO @ Tue, 16 Jun 2020 09:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:13: 12000000 INFO @ Tue, 16 Jun 2020 09:12:13: 6000000 INFO @ Tue, 16 Jun 2020 09:12:14: #2 number of paired peaks: 207 WARNING @ Tue, 16 Jun 2020 09:12:14: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:14: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:12:14: #2 alternative fragment length(s) may be 1,36,567,592 bps INFO @ Tue, 16 Jun 2020 09:12:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:14: #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 09:12:14: #2 You may need to consider one of the other alternative d(s): 1,36,567,592 WARNING @ Tue, 16 Jun 2020 09:12:14: #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 09:12:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:19: 7000000 INFO @ Tue, 16 Jun 2020 09:12:19: 13000000 INFO @ Tue, 16 Jun 2020 09:12:24: 8000000 INFO @ Tue, 16 Jun 2020 09:12:24: 14000000 INFO @ Tue, 16 Jun 2020 09:12:29: 9000000 INFO @ Tue, 16 Jun 2020 09:12:30: 15000000 INFO @ Tue, 16 Jun 2020 09:12:35: 10000000 INFO @ Tue, 16 Jun 2020 09:12:35: 16000000 INFO @ Tue, 16 Jun 2020 09:12:40: 11000000 INFO @ Tue, 16 Jun 2020 09:12:41: 17000000 INFO @ Tue, 16 Jun 2020 09:12:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:44: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:44: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:44: #1 total tags in treatment: 17587108 INFO @ Tue, 16 Jun 2020 09:12:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:44: #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 09:12:44: #1 tags after filtering in treatment: 17587108 INFO @ Tue, 16 Jun 2020 09:12:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:46: #2 number of paired peaks: 207 WARNING @ Tue, 16 Jun 2020 09:12:46: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:46: 12000000 INFO @ Tue, 16 Jun 2020 09:12:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:46: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:12:46: #2 alternative fragment length(s) may be 1,36,567,592 bps INFO @ Tue, 16 Jun 2020 09:12:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:46: #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 09:12:46: #2 You may need to consider one of the other alternative d(s): 1,36,567,592 WARNING @ Tue, 16 Jun 2020 09:12:46: #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 09:12:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:51: 13000000 INFO @ Tue, 16 Jun 2020 09:12:56: 14000000 INFO @ Tue, 16 Jun 2020 09:12:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:57: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:01: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:06: 16000000 INFO @ Tue, 16 Jun 2020 09:13:11: 17000000 INFO @ Tue, 16 Jun 2020 09:13:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:15: #1 total tags in treatment: 17587108 INFO @ Tue, 16 Jun 2020 09:13:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:15: #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 09:13:15: #1 tags after filtering in treatment: 17587108 INFO @ Tue, 16 Jun 2020 09:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:16: #2 number of paired peaks: 207 WARNING @ Tue, 16 Jun 2020 09:13:16: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:16: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:13:16: #2 alternative fragment length(s) may be 1,36,567,592 bps INFO @ Tue, 16 Jun 2020 09:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:16: #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 09:13:16: #2 You may need to consider one of the other alternative d(s): 1,36,567,592 WARNING @ Tue, 16 Jun 2020 09:13:16: #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 09:13:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494845/SRX494845.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling