Job ID = 6497408 SRX = SRX494820 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:57:09 prefetch.2.10.7: 1) Downloading 'SRR1198352'... 2020-06-25T21:57:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:59:14 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:59:14 prefetch.2.10.7: 1) 'SRR1198352' was downloaded successfully Read 19263987 spots for SRR1198352/SRR1198352.sra Written 19263987 spots for SRR1198352/SRR1198352.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: 00:00:01 Multiseed full-index search: 00:03:49 19263987 reads; of these: 19263987 (100.00%) were unpaired; of these: 287261 (1.49%) aligned 0 times 15656582 (81.27%) aligned exactly 1 time 3320144 (17.23%) aligned >1 times 98.51% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 1890339 / 18976726 = 0.0996 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 @ Fri, 26 Jun 2020 07:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.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 @ Fri, 26 Jun 2020 07:09:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:09:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:09:59: 1000000 INFO @ Fri, 26 Jun 2020 07:10:04: 2000000 INFO @ Fri, 26 Jun 2020 07:10:10: 3000000 INFO @ Fri, 26 Jun 2020 07:10:15: 4000000 INFO @ Fri, 26 Jun 2020 07:10:21: 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 @ Fri, 26 Jun 2020 07:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.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 @ Fri, 26 Jun 2020 07:10:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:10:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:10:27: 6000000 INFO @ Fri, 26 Jun 2020 07:10:29: 1000000 INFO @ Fri, 26 Jun 2020 07:10:32: 7000000 INFO @ Fri, 26 Jun 2020 07:10:34: 2000000 INFO @ Fri, 26 Jun 2020 07:10:38: 8000000 INFO @ Fri, 26 Jun 2020 07:10:40: 3000000 INFO @ Fri, 26 Jun 2020 07:10:43: 9000000 INFO @ Fri, 26 Jun 2020 07:10:46: 4000000 INFO @ Fri, 26 Jun 2020 07:10:49: 10000000 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 @ Fri, 26 Jun 2020 07:10:52: 5000000 INFO @ Fri, 26 Jun 2020 07:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.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 @ Fri, 26 Jun 2020 07:10:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:10:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:10:54: 11000000 INFO @ Fri, 26 Jun 2020 07:10:57: 6000000 INFO @ Fri, 26 Jun 2020 07:10:59: 1000000 INFO @ Fri, 26 Jun 2020 07:11:00: 12000000 INFO @ Fri, 26 Jun 2020 07:11:03: 7000000 INFO @ Fri, 26 Jun 2020 07:11:05: 2000000 INFO @ Fri, 26 Jun 2020 07:11:06: 13000000 INFO @ Fri, 26 Jun 2020 07:11:09: 8000000 INFO @ Fri, 26 Jun 2020 07:11:10: 3000000 INFO @ Fri, 26 Jun 2020 07:11:12: 14000000 INFO @ Fri, 26 Jun 2020 07:11:15: 9000000 INFO @ Fri, 26 Jun 2020 07:11:17: 4000000 INFO @ Fri, 26 Jun 2020 07:11:17: 15000000 INFO @ Fri, 26 Jun 2020 07:11:20: 10000000 INFO @ Fri, 26 Jun 2020 07:11:23: 5000000 INFO @ Fri, 26 Jun 2020 07:11:23: 16000000 INFO @ Fri, 26 Jun 2020 07:11:26: 11000000 INFO @ Fri, 26 Jun 2020 07:11:28: 6000000 INFO @ Fri, 26 Jun 2020 07:11:29: 17000000 INFO @ Fri, 26 Jun 2020 07:11:29: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:11:29: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:11:29: #1 total tags in treatment: 17086387 INFO @ Fri, 26 Jun 2020 07:11:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:11:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:11:30: #1 tags after filtering in treatment: 17086387 INFO @ Fri, 26 Jun 2020 07:11:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:11:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:11:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:11:31: #2 number of paired peaks: 175 WARNING @ Fri, 26 Jun 2020 07:11:31: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 26 Jun 2020 07:11:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:11:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:11:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:11:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:11:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:11:31: #2 alternative fragment length(s) may be 1,31,534,559 bps INFO @ Fri, 26 Jun 2020 07:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.05_model.r WARNING @ Fri, 26 Jun 2020 07:11:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:11:31: #2 You may need to consider one of the other alternative d(s): 1,31,534,559 WARNING @ Fri, 26 Jun 2020 07:11:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:11:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:11:32: 12000000 INFO @ Fri, 26 Jun 2020 07:11:34: 7000000 INFO @ Fri, 26 Jun 2020 07:11:37: 13000000 INFO @ Fri, 26 Jun 2020 07:11:40: 8000000 INFO @ Fri, 26 Jun 2020 07:11:43: 14000000 INFO @ Fri, 26 Jun 2020 07:11:45: 9000000 INFO @ Fri, 26 Jun 2020 07:11:49: 15000000 INFO @ Fri, 26 Jun 2020 07:11:51: 10000000 INFO @ Fri, 26 Jun 2020 07:11:54: 16000000 INFO @ Fri, 26 Jun 2020 07:11:57: 11000000 INFO @ Fri, 26 Jun 2020 07:12:00: 17000000 INFO @ Fri, 26 Jun 2020 07:12:00: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:12:00: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:12:00: #1 total tags in treatment: 17086387 INFO @ Fri, 26 Jun 2020 07:12:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:12:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:12:01: #1 tags after filtering in treatment: 17086387 INFO @ Fri, 26 Jun 2020 07:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:01: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:02: #2 number of paired peaks: 175 WARNING @ Fri, 26 Jun 2020 07:12:02: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:02: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:02: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:02: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:02: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:02: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:12:02: #2 alternative fragment length(s) may be 1,31,534,559 bps INFO @ Fri, 26 Jun 2020 07:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.10_model.r WARNING @ Fri, 26 Jun 2020 07:12:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:02: #2 You may need to consider one of the other alternative d(s): 1,31,534,559 WARNING @ Fri, 26 Jun 2020 07:12:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:12:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:02: 12000000 INFO @ Fri, 26 Jun 2020 07:12:07: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:12:13: 14000000 INFO @ Fri, 26 Jun 2020 07:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.05_summits.bed INFO @ Fri, 26 Jun 2020 07:12:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:12:18: 15000000 INFO @ Fri, 26 Jun 2020 07:12:24: 16000000 INFO @ Fri, 26 Jun 2020 07:12:29: 17000000 INFO @ Fri, 26 Jun 2020 07:12:30: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:12:30: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:12:30: #1 total tags in treatment: 17086387 INFO @ Fri, 26 Jun 2020 07:12:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:12:30: #1 tags after filtering in treatment: 17086387 INFO @ Fri, 26 Jun 2020 07:12:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:12:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:12:31: #2 number of paired peaks: 175 WARNING @ Fri, 26 Jun 2020 07:12:31: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:12:31: #2 alternative fragment length(s) may be 1,31,534,559 bps INFO @ Fri, 26 Jun 2020 07:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.20_model.r WARNING @ Fri, 26 Jun 2020 07:12:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:31: #2 You may need to consider one of the other alternative d(s): 1,31,534,559 WARNING @ Fri, 26 Jun 2020 07:12:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:12:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.10_summits.bed INFO @ Fri, 26 Jun 2020 07:12:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:13:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494820/SRX494820.20_summits.bed INFO @ Fri, 26 Jun 2020 07:13:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling