Job ID = 6507892 SRX = SRX494977 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:19:19 prefetch.2.10.7: 1) Downloading 'SRR1198509'... 2020-06-26T13:19:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:22:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:22:30 prefetch.2.10.7: 1) 'SRR1198509' was downloaded successfully Read 29285047 spots for SRR1198509/SRR1198509.sra Written 29285047 spots for SRR1198509/SRR1198509.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: 00:07:04 29285047 reads; of these: 29285047 (100.00%) were unpaired; of these: 1130170 (3.86%) aligned 0 times 23737579 (81.06%) aligned exactly 1 time 4417298 (15.08%) aligned >1 times 96.14% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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 12 files... [bam_rmdupse_core] 11075869 / 28154877 = 0.3934 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 22:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.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 22:37:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:31: 1000000 INFO @ Fri, 26 Jun 2020 22:37:37: 2000000 INFO @ Fri, 26 Jun 2020 22:37:44: 3000000 INFO @ Fri, 26 Jun 2020 22:37:50: 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 22:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.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 22:37:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:56: 5000000 INFO @ Fri, 26 Jun 2020 22:38:02: 1000000 INFO @ Fri, 26 Jun 2020 22:38:03: 6000000 INFO @ Fri, 26 Jun 2020 22:38:09: 2000000 INFO @ Fri, 26 Jun 2020 22:38:10: 7000000 INFO @ Fri, 26 Jun 2020 22:38:16: 3000000 INFO @ Fri, 26 Jun 2020 22:38:16: 8000000 INFO @ Fri, 26 Jun 2020 22:38:23: 4000000 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 22:38:23: 9000000 INFO @ Fri, 26 Jun 2020 22:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.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 22:38:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:38:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:38:30: 5000000 INFO @ Fri, 26 Jun 2020 22:38:30: 10000000 INFO @ Fri, 26 Jun 2020 22:38:32: 1000000 INFO @ Fri, 26 Jun 2020 22:38:37: 11000000 INFO @ Fri, 26 Jun 2020 22:38:37: 6000000 INFO @ Fri, 26 Jun 2020 22:38:40: 2000000 INFO @ Fri, 26 Jun 2020 22:38:44: 12000000 INFO @ Fri, 26 Jun 2020 22:38:44: 7000000 INFO @ Fri, 26 Jun 2020 22:38:47: 3000000 INFO @ Fri, 26 Jun 2020 22:38:51: 13000000 INFO @ Fri, 26 Jun 2020 22:38:51: 8000000 INFO @ Fri, 26 Jun 2020 22:38:54: 4000000 INFO @ Fri, 26 Jun 2020 22:38:57: 14000000 INFO @ Fri, 26 Jun 2020 22:38:58: 9000000 INFO @ Fri, 26 Jun 2020 22:39:01: 5000000 INFO @ Fri, 26 Jun 2020 22:39:04: 15000000 INFO @ Fri, 26 Jun 2020 22:39:05: 10000000 INFO @ Fri, 26 Jun 2020 22:39:07: 6000000 INFO @ Fri, 26 Jun 2020 22:39:11: 16000000 INFO @ Fri, 26 Jun 2020 22:39:12: 11000000 INFO @ Fri, 26 Jun 2020 22:39:14: 7000000 INFO @ Fri, 26 Jun 2020 22:39:18: 17000000 INFO @ Fri, 26 Jun 2020 22:39:18: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:39:18: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:39:18: #1 total tags in treatment: 17079008 INFO @ Fri, 26 Jun 2020 22:39:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:18: #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 22:39:18: 12000000 INFO @ Fri, 26 Jun 2020 22:39:19: #1 tags after filtering in treatment: 17079008 INFO @ Fri, 26 Jun 2020 22:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:20: #2 number of paired peaks: 191 WARNING @ Fri, 26 Jun 2020 22:39:20: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:20: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:39:20: #2 alternative fragment length(s) may be 1,11,29,47,102,474,548 bps INFO @ Fri, 26 Jun 2020 22:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.05_model.r WARNING @ Fri, 26 Jun 2020 22:39:20: #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 22:39:20: #2 You may need to consider one of the other alternative d(s): 1,11,29,47,102,474,548 WARNING @ Fri, 26 Jun 2020 22:39:20: #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 22:39:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:21: 8000000 INFO @ Fri, 26 Jun 2020 22:39:25: 13000000 INFO @ Fri, 26 Jun 2020 22:39:27: 9000000 INFO @ Fri, 26 Jun 2020 22:39:31: 14000000 INFO @ Fri, 26 Jun 2020 22:39:34: 10000000 INFO @ Fri, 26 Jun 2020 22:39:38: 15000000 INFO @ Fri, 26 Jun 2020 22:39:40: 11000000 INFO @ Fri, 26 Jun 2020 22:39:44: 16000000 INFO @ Fri, 26 Jun 2020 22:39:46: 12000000 INFO @ Fri, 26 Jun 2020 22:39:50: 17000000 INFO @ Fri, 26 Jun 2020 22:39:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:39:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:39:51: #1 total tags in treatment: 17079008 INFO @ Fri, 26 Jun 2020 22:39:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:51: #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 22:39:51: #1 tags after filtering in treatment: 17079008 INFO @ Fri, 26 Jun 2020 22:39:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:51: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:52: #2 number of paired peaks: 191 WARNING @ Fri, 26 Jun 2020 22:39:52: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:52: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:52: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:52: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:52: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:52: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:39:52: #2 alternative fragment length(s) may be 1,11,29,47,102,474,548 bps INFO @ Fri, 26 Jun 2020 22:39:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.10_model.r WARNING @ Fri, 26 Jun 2020 22:39:52: #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 22:39:52: #2 You may need to consider one of the other alternative d(s): 1,11,29,47,102,474,548 WARNING @ Fri, 26 Jun 2020 22:39:52: #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 22:39:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:53: 13000000 INFO @ Fri, 26 Jun 2020 22:39:59: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:40:05: 15000000 INFO @ Fri, 26 Jun 2020 22:40:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.05_summits.bed INFO @ Fri, 26 Jun 2020 22:40:06: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:40:11: 16000000 INFO @ Fri, 26 Jun 2020 22:40:17: 17000000 INFO @ Fri, 26 Jun 2020 22:40:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:40:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:40:17: #1 total tags in treatment: 17079008 INFO @ Fri, 26 Jun 2020 22:40:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:40:17: #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 22:40:17: #1 tags after filtering in treatment: 17079008 INFO @ Fri, 26 Jun 2020 22:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:40:17: #1 finished! INFO @ Fri, 26 Jun 2020 22:40:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:40:19: #2 number of paired peaks: 191 WARNING @ Fri, 26 Jun 2020 22:40:19: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 26 Jun 2020 22:40:19: start model_add_line... INFO @ Fri, 26 Jun 2020 22:40:19: start X-correlation... INFO @ Fri, 26 Jun 2020 22:40:19: end of X-cor INFO @ Fri, 26 Jun 2020 22:40:19: #2 finished! INFO @ Fri, 26 Jun 2020 22:40:19: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:40:19: #2 alternative fragment length(s) may be 1,11,29,47,102,474,548 bps INFO @ Fri, 26 Jun 2020 22:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.20_model.r WARNING @ Fri, 26 Jun 2020 22:40:19: #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 22:40:19: #2 You may need to consider one of the other alternative d(s): 1,11,29,47,102,474,548 WARNING @ Fri, 26 Jun 2020 22:40:19: #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 22:40:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:40:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.10_summits.bed INFO @ Fri, 26 Jun 2020 22:40:38: 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 22:40:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494977/SRX494977.20_summits.bed INFO @ Fri, 26 Jun 2020 22:41:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling