Job ID = 6367708 SRX = SRX395532 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:20 prefetch.2.10.7: 1) Downloading 'SRR1054265'... 2020-06-15T23:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:28 prefetch.2.10.7: 'SRR1054265' is valid 2020-06-15T23:34:28 prefetch.2.10.7: 1) 'SRR1054265' was downloaded successfully Read 6861156 spots for SRR1054265/SRR1054265.sra Written 6861156 spots for SRR1054265/SRR1054265.sra 2020-06-15T23:34:57 prefetch.2.10.7: 1) Downloading 'SRR1054266'... 2020-06-15T23:34:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:12 prefetch.2.10.7: 'SRR1054266' is valid 2020-06-15T23:36:12 prefetch.2.10.7: 1) 'SRR1054266' was downloaded successfully Read 5956085 spots for SRR1054266/SRR1054266.sra Written 5956085 spots for SRR1054266/SRR1054266.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: 00:01:59 12817241 reads; of these: 12817241 (100.00%) were unpaired; of these: 103768 (0.81%) aligned 0 times 10660319 (83.17%) aligned exactly 1 time 2053154 (16.02%) aligned >1 times 99.19% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 1211991 / 12713473 = 0.0953 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 08:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.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 08:41:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:30: 1000000 INFO @ Tue, 16 Jun 2020 08:41:35: 2000000 INFO @ Tue, 16 Jun 2020 08:41:39: 3000000 INFO @ Tue, 16 Jun 2020 08:41:44: 4000000 INFO @ Tue, 16 Jun 2020 08:41:48: 5000000 INFO @ Tue, 16 Jun 2020 08:41:53: 6000000 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 08:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.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 08:41:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:58: 7000000 INFO @ Tue, 16 Jun 2020 08:42:01: 1000000 INFO @ Tue, 16 Jun 2020 08:42:02: 8000000 INFO @ Tue, 16 Jun 2020 08:42:06: 2000000 INFO @ Tue, 16 Jun 2020 08:42:07: 9000000 INFO @ Tue, 16 Jun 2020 08:42:11: 3000000 INFO @ Tue, 16 Jun 2020 08:42:12: 10000000 INFO @ Tue, 16 Jun 2020 08:42:16: 4000000 INFO @ Tue, 16 Jun 2020 08:42:17: 11000000 INFO @ Tue, 16 Jun 2020 08:42:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:19: #1 total tags in treatment: 11501482 INFO @ Tue, 16 Jun 2020 08:42:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:19: #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 08:42:20: #1 tags after filtering in treatment: 11501482 INFO @ Tue, 16 Jun 2020 08:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:20: 5000000 INFO @ Tue, 16 Jun 2020 08:42:20: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:42:20: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:42:21: #2 alternative fragment length(s) may be 1,26,551,579 bps INFO @ Tue, 16 Jun 2020 08:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.05_model.r WARNING @ Tue, 16 Jun 2020 08:42:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:21: #2 You may need to consider one of the other alternative d(s): 1,26,551,579 WARNING @ Tue, 16 Jun 2020 08:42:21: #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 08:42:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:21: #3 Pre-compute pvalue-qvalue table... 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 08:42:25: 6000000 INFO @ Tue, 16 Jun 2020 08:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.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 08:42:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:30: 7000000 INFO @ Tue, 16 Jun 2020 08:42:31: 1000000 INFO @ Tue, 16 Jun 2020 08:42:35: 8000000 INFO @ Tue, 16 Jun 2020 08:42:36: 2000000 INFO @ Tue, 16 Jun 2020 08:42:40: 9000000 INFO @ Tue, 16 Jun 2020 08:42:41: 3000000 INFO @ Tue, 16 Jun 2020 08:42:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:45: 10000000 INFO @ Tue, 16 Jun 2020 08:42:46: 4000000 INFO @ Tue, 16 Jun 2020 08:42:50: 11000000 INFO @ Tue, 16 Jun 2020 08:42:50: 5000000 INFO @ Tue, 16 Jun 2020 08:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:52: #1 total tags in treatment: 11501482 INFO @ Tue, 16 Jun 2020 08:42:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:52: #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 08:42:52: #1 tags after filtering in treatment: 11501482 INFO @ Tue, 16 Jun 2020 08:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:53: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:42:53: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:53: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:42:53: #2 alternative fragment length(s) may be 1,26,551,579 bps INFO @ Tue, 16 Jun 2020 08:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.10_model.r WARNING @ Tue, 16 Jun 2020 08:42:53: #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 08:42:53: #2 You may need to consider one of the other alternative d(s): 1,26,551,579 WARNING @ Tue, 16 Jun 2020 08:42:53: #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 08:42:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:55: 6000000 INFO @ Tue, 16 Jun 2020 08:43:00: 7000000 INFO @ Tue, 16 Jun 2020 08:43:05: 8000000 INFO @ Tue, 16 Jun 2020 08:43:09: 9000000 INFO @ Tue, 16 Jun 2020 08:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:14: 10000000 INFO @ Tue, 16 Jun 2020 08:43:19: 11000000 INFO @ Tue, 16 Jun 2020 08:43:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:21: #1 total tags in treatment: 11501482 INFO @ Tue, 16 Jun 2020 08:43:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:21: #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 08:43:21: #1 tags after filtering in treatment: 11501482 INFO @ Tue, 16 Jun 2020 08:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:22: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:43:22: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:43:22: #2 alternative fragment length(s) may be 1,26,551,579 bps INFO @ Tue, 16 Jun 2020 08:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.20_model.r WARNING @ Tue, 16 Jun 2020 08:43:22: #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 08:43:22: #2 You may need to consider one of the other alternative d(s): 1,26,551,579 WARNING @ Tue, 16 Jun 2020 08:43:22: #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 08:43:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.10_summits.bed INFO @ Tue, 16 Jun 2020 08:43:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395532/SRX395532.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling