Job ID = 6366857 SRX = SRX2350756 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:01 prefetch.2.10.7: 1) Downloading 'SRR5024065'... 2020-06-15T23:14:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:49 prefetch.2.10.7: 'SRR5024065' is valid 2020-06-15T23:15:49 prefetch.2.10.7: 1) 'SRR5024065' was downloaded successfully Read 12463337 spots for SRR5024065/SRR5024065.sra Written 12463337 spots for SRR5024065/SRR5024065.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: 00:03:02 12463337 reads; of these: 12463337 (100.00%) were unpaired; of these: 133672 (1.07%) aligned 0 times 10819121 (86.81%) aligned exactly 1 time 1510544 (12.12%) aligned >1 times 98.93% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 1826641 / 12329665 = 0.1482 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 08:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.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 08:23:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:10: 1000000 INFO @ Tue, 16 Jun 2020 08:23:17: 2000000 INFO @ Tue, 16 Jun 2020 08:23:23: 3000000 INFO @ Tue, 16 Jun 2020 08:23:30: 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 @ Tue, 16 Jun 2020 08:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.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 08:23:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:37: 5000000 INFO @ Tue, 16 Jun 2020 08:23:41: 1000000 INFO @ Tue, 16 Jun 2020 08:23:45: 6000000 INFO @ Tue, 16 Jun 2020 08:23:48: 2000000 INFO @ Tue, 16 Jun 2020 08:23:52: 7000000 INFO @ Tue, 16 Jun 2020 08:23:55: 3000000 INFO @ Tue, 16 Jun 2020 08:23:59: 8000000 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 08:24:02: 4000000 INFO @ Tue, 16 Jun 2020 08:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.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 08:24:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:07: 9000000 INFO @ Tue, 16 Jun 2020 08:24:10: 5000000 INFO @ Tue, 16 Jun 2020 08:24:11: 1000000 INFO @ Tue, 16 Jun 2020 08:24:14: 10000000 INFO @ Tue, 16 Jun 2020 08:24:17: 6000000 INFO @ Tue, 16 Jun 2020 08:24:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:17: #1 total tags in treatment: 10503024 INFO @ Tue, 16 Jun 2020 08:24:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:17: #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 08:24:18: #1 tags after filtering in treatment: 10503024 INFO @ Tue, 16 Jun 2020 08:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:18: 2000000 INFO @ Tue, 16 Jun 2020 08:24:18: #2 number of paired peaks: 121 WARNING @ Tue, 16 Jun 2020 08:24:18: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:18: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:24:18: #2 alternative fragment length(s) may be 3,48,387,432,468,492,523,568 bps INFO @ Tue, 16 Jun 2020 08:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.05_model.r WARNING @ Tue, 16 Jun 2020 08:24:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:19: #2 You may need to consider one of the other alternative d(s): 3,48,387,432,468,492,523,568 WARNING @ Tue, 16 Jun 2020 08:24:19: #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 08:24:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:24: 7000000 INFO @ Tue, 16 Jun 2020 08:24:25: 3000000 INFO @ Tue, 16 Jun 2020 08:24:31: 8000000 INFO @ Tue, 16 Jun 2020 08:24:32: 4000000 INFO @ Tue, 16 Jun 2020 08:24:38: 9000000 INFO @ Tue, 16 Jun 2020 08:24:39: 5000000 INFO @ Tue, 16 Jun 2020 08:24:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:45: 10000000 INFO @ Tue, 16 Jun 2020 08:24:46: 6000000 INFO @ Tue, 16 Jun 2020 08:24:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:49: #1 total tags in treatment: 10503024 INFO @ Tue, 16 Jun 2020 08:24:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:49: #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 08:24:49: #1 tags after filtering in treatment: 10503024 INFO @ Tue, 16 Jun 2020 08:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:50: #2 number of paired peaks: 121 WARNING @ Tue, 16 Jun 2020 08:24:50: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:50: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:24:50: #2 alternative fragment length(s) may be 3,48,387,432,468,492,523,568 bps INFO @ Tue, 16 Jun 2020 08:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.10_model.r WARNING @ Tue, 16 Jun 2020 08:24:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:50: #2 You may need to consider one of the other alternative d(s): 3,48,387,432,468,492,523,568 WARNING @ Tue, 16 Jun 2020 08:24:50: #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 08:24:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (696 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:59: 8000000 INFO @ Tue, 16 Jun 2020 08:25:06: 9000000 INFO @ Tue, 16 Jun 2020 08:25:12: 10000000 INFO @ Tue, 16 Jun 2020 08:25:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:15: #1 total tags in treatment: 10503024 INFO @ Tue, 16 Jun 2020 08:25:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:15: #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 08:25:15: #1 tags after filtering in treatment: 10503024 INFO @ Tue, 16 Jun 2020 08:25:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:16: #2 number of paired peaks: 121 WARNING @ Tue, 16 Jun 2020 08:25:16: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:16: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:25:16: #2 alternative fragment length(s) may be 3,48,387,432,468,492,523,568 bps INFO @ Tue, 16 Jun 2020 08:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.20_model.r WARNING @ Tue, 16 Jun 2020 08:25:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:16: #2 You may need to consider one of the other alternative d(s): 3,48,387,432,468,492,523,568 WARNING @ Tue, 16 Jun 2020 08:25:16: #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 08:25:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350756/SRX2350756.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 1 millis CompletedMACS2peakCalling