Job ID = 6507866 SRX = SRX494947 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:05:32 prefetch.2.10.7: 1) Downloading 'SRR1198479'... 2020-06-26T13:05:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:06:41 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:06:42 prefetch.2.10.7: 'SRR1198479' is valid 2020-06-26T13:06:42 prefetch.2.10.7: 1) 'SRR1198479' was downloaded successfully Read 15863850 spots for SRR1198479/SRR1198479.sra Written 15863850 spots for SRR1198479/SRR1198479.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: 00:02:57 15863850 reads; of these: 15863850 (100.00%) were unpaired; of these: 231741 (1.46%) aligned 0 times 12990289 (81.89%) aligned exactly 1 time 2641820 (16.65%) aligned >1 times 98.54% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_rmdupse_core] 1436443 / 15632109 = 0.0919 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 22:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.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 22:14:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:14:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:14:13: 1000000 INFO @ Fri, 26 Jun 2020 22:14:19: 2000000 INFO @ Fri, 26 Jun 2020 22:14:25: 3000000 INFO @ Fri, 26 Jun 2020 22:14:30: 4000000 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 22:14:36: 5000000 INFO @ Fri, 26 Jun 2020 22:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.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 22:14:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:14:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:14:43: 6000000 INFO @ Fri, 26 Jun 2020 22:14:45: 1000000 INFO @ Fri, 26 Jun 2020 22:14:49: 7000000 INFO @ Fri, 26 Jun 2020 22:14:52: 2000000 INFO @ Fri, 26 Jun 2020 22:14:56: 8000000 INFO @ Fri, 26 Jun 2020 22:14:59: 3000000 INFO @ Fri, 26 Jun 2020 22:15:03: 9000000 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 22:15:06: 4000000 INFO @ Fri, 26 Jun 2020 22:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.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 22:15:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:15:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:15:10: 10000000 INFO @ Fri, 26 Jun 2020 22:15:14: 5000000 INFO @ Fri, 26 Jun 2020 22:15:15: 1000000 INFO @ Fri, 26 Jun 2020 22:15:16: 11000000 INFO @ Fri, 26 Jun 2020 22:15:21: 6000000 INFO @ Fri, 26 Jun 2020 22:15:22: 2000000 INFO @ Fri, 26 Jun 2020 22:15:23: 12000000 INFO @ Fri, 26 Jun 2020 22:15:28: 7000000 INFO @ Fri, 26 Jun 2020 22:15:29: 3000000 INFO @ Fri, 26 Jun 2020 22:15:30: 13000000 INFO @ Fri, 26 Jun 2020 22:15:36: 8000000 INFO @ Fri, 26 Jun 2020 22:15:36: 4000000 INFO @ Fri, 26 Jun 2020 22:15:37: 14000000 INFO @ Fri, 26 Jun 2020 22:15:38: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:15:38: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:15:38: #1 total tags in treatment: 14195666 INFO @ Fri, 26 Jun 2020 22:15:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:15:38: #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 22:15:38: #1 tags after filtering in treatment: 14195666 INFO @ Fri, 26 Jun 2020 22:15:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:15:38: #1 finished! INFO @ Fri, 26 Jun 2020 22:15:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:15:39: #2 number of paired peaks: 251 WARNING @ Fri, 26 Jun 2020 22:15:39: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 26 Jun 2020 22:15:39: start model_add_line... INFO @ Fri, 26 Jun 2020 22:15:39: start X-correlation... INFO @ Fri, 26 Jun 2020 22:15:39: end of X-cor INFO @ Fri, 26 Jun 2020 22:15:39: #2 finished! INFO @ Fri, 26 Jun 2020 22:15:39: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:15:39: #2 alternative fragment length(s) may be 1,30,559,593 bps INFO @ Fri, 26 Jun 2020 22:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.05_model.r WARNING @ Fri, 26 Jun 2020 22:15:39: #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 22:15:39: #2 You may need to consider one of the other alternative d(s): 1,30,559,593 WARNING @ Fri, 26 Jun 2020 22:15:39: #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 22:15:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:15:43: 9000000 INFO @ Fri, 26 Jun 2020 22:15:43: 5000000 INFO @ Fri, 26 Jun 2020 22:15:50: 10000000 INFO @ Fri, 26 Jun 2020 22:15:51: 6000000 INFO @ Fri, 26 Jun 2020 22:15:57: 11000000 INFO @ Fri, 26 Jun 2020 22:15:58: 7000000 INFO @ Fri, 26 Jun 2020 22:16:04: 12000000 INFO @ Fri, 26 Jun 2020 22:16:05: 8000000 INFO @ Fri, 26 Jun 2020 22:16:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:16:12: 13000000 INFO @ Fri, 26 Jun 2020 22:16:12: 9000000 INFO @ Fri, 26 Jun 2020 22:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.05_summits.bed INFO @ Fri, 26 Jun 2020 22:16:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:16:19: 14000000 INFO @ Fri, 26 Jun 2020 22:16:19: 10000000 INFO @ Fri, 26 Jun 2020 22:16:20: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:16:20: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:16:20: #1 total tags in treatment: 14195666 INFO @ Fri, 26 Jun 2020 22:16:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:16:20: #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 22:16:20: #1 tags after filtering in treatment: 14195666 INFO @ Fri, 26 Jun 2020 22:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:16:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:16:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:16:21: #2 number of paired peaks: 251 WARNING @ Fri, 26 Jun 2020 22:16:21: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 26 Jun 2020 22:16:21: start model_add_line... INFO @ Fri, 26 Jun 2020 22:16:21: start X-correlation... INFO @ Fri, 26 Jun 2020 22:16:21: end of X-cor INFO @ Fri, 26 Jun 2020 22:16:21: #2 finished! INFO @ Fri, 26 Jun 2020 22:16:21: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:16:21: #2 alternative fragment length(s) may be 1,30,559,593 bps INFO @ Fri, 26 Jun 2020 22:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.10_model.r WARNING @ Fri, 26 Jun 2020 22:16:21: #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 22:16:21: #2 You may need to consider one of the other alternative d(s): 1,30,559,593 WARNING @ Fri, 26 Jun 2020 22:16:21: #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 22:16:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:16:25: 11000000 INFO @ Fri, 26 Jun 2020 22:16:32: 12000000 INFO @ Fri, 26 Jun 2020 22:16:38: 13000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:16:44: 14000000 INFO @ Fri, 26 Jun 2020 22:16:46: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:16:46: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:16:46: #1 total tags in treatment: 14195666 INFO @ Fri, 26 Jun 2020 22:16:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:16:46: #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 22:16:46: #1 tags after filtering in treatment: 14195666 INFO @ Fri, 26 Jun 2020 22:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:16:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:16:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:16:47: #2 number of paired peaks: 251 WARNING @ Fri, 26 Jun 2020 22:16:47: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 26 Jun 2020 22:16:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:16:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:16:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:16:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:16:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:16:47: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:16:47: #2 alternative fragment length(s) may be 1,30,559,593 bps INFO @ Fri, 26 Jun 2020 22:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.20_model.r WARNING @ Fri, 26 Jun 2020 22:16:47: #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 22:16:47: #2 You may need to consider one of the other alternative d(s): 1,30,559,593 WARNING @ Fri, 26 Jun 2020 22:16:47: #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 22:16:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.10_summits.bed INFO @ Fri, 26 Jun 2020 22:16:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:17:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:17:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:17:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:17:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494947/SRX494947.20_summits.bed INFO @ Fri, 26 Jun 2020 22:17:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling