Job ID = 6368607 SRX = SRX5020832 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:33 prefetch.2.10.7: 1) Downloading 'SRR8201455'... 2020-06-16T00:23:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:15 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:16 prefetch.2.10.7: 'SRR8201455' is valid 2020-06-16T00:25:16 prefetch.2.10.7: 1) 'SRR8201455' was downloaded successfully 2020-06-16T00:25:16 prefetch.2.10.7: 'SRR8201455' has 0 unresolved dependencies Read 16729964 spots for SRR8201455/SRR8201455.sra Written 16729964 spots for SRR8201455/SRR8201455.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: 00:03:32 16729964 reads; of these: 16729964 (100.00%) were unpaired; of these: 1123557 (6.72%) aligned 0 times 13217766 (79.01%) aligned exactly 1 time 2388641 (14.28%) aligned >1 times 93.28% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 1991023 / 15606407 = 0.1276 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 09:33:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.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 09:33:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:37: 1000000 INFO @ Tue, 16 Jun 2020 09:33:43: 2000000 INFO @ Tue, 16 Jun 2020 09:33:49: 3000000 INFO @ Tue, 16 Jun 2020 09:33:55: 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 09:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.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 09:34:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:01: 5000000 INFO @ Tue, 16 Jun 2020 09:34:07: 1000000 INFO @ Tue, 16 Jun 2020 09:34:08: 6000000 INFO @ Tue, 16 Jun 2020 09:34:14: 2000000 INFO @ Tue, 16 Jun 2020 09:34:14: 7000000 INFO @ Tue, 16 Jun 2020 09:34:20: 3000000 INFO @ Tue, 16 Jun 2020 09:34:21: 8000000 INFO @ Tue, 16 Jun 2020 09:34:27: 4000000 INFO @ Tue, 16 Jun 2020 09:34:28: 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 @ Tue, 16 Jun 2020 09:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.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 09:34:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:34: 5000000 INFO @ Tue, 16 Jun 2020 09:34:34: 10000000 INFO @ Tue, 16 Jun 2020 09:34:37: 1000000 INFO @ Tue, 16 Jun 2020 09:34:40: 6000000 INFO @ Tue, 16 Jun 2020 09:34:41: 11000000 INFO @ Tue, 16 Jun 2020 09:34:43: 2000000 INFO @ Tue, 16 Jun 2020 09:34:47: 7000000 INFO @ Tue, 16 Jun 2020 09:34:47: 12000000 INFO @ Tue, 16 Jun 2020 09:34:50: 3000000 INFO @ Tue, 16 Jun 2020 09:34:54: 8000000 INFO @ Tue, 16 Jun 2020 09:34:54: 13000000 INFO @ Tue, 16 Jun 2020 09:34:56: 4000000 INFO @ Tue, 16 Jun 2020 09:34:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:58: #1 total tags in treatment: 13615384 INFO @ Tue, 16 Jun 2020 09:34:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:58: #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 09:34:58: #1 tags after filtering in treatment: 13615384 INFO @ Tue, 16 Jun 2020 09:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:59: #2 number of paired peaks: 246 WARNING @ Tue, 16 Jun 2020 09:34:59: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:59: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:34:59: #2 alternative fragment length(s) may be 2,45,566 bps INFO @ Tue, 16 Jun 2020 09:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:59: #2 You may need to consider one of the other alternative d(s): 2,45,566 WARNING @ Tue, 16 Jun 2020 09:34:59: #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 09:34:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:00: 9000000 INFO @ Tue, 16 Jun 2020 09:35:02: 5000000 INFO @ Tue, 16 Jun 2020 09:35:07: 10000000 INFO @ Tue, 16 Jun 2020 09:35:08: 6000000 INFO @ Tue, 16 Jun 2020 09:35:14: 11000000 INFO @ Tue, 16 Jun 2020 09:35:15: 7000000 INFO @ Tue, 16 Jun 2020 09:35:20: 12000000 INFO @ Tue, 16 Jun 2020 09:35:21: 8000000 INFO @ Tue, 16 Jun 2020 09:35:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:27: 9000000 INFO @ Tue, 16 Jun 2020 09:35:27: 13000000 INFO @ Tue, 16 Jun 2020 09:35:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:31: #1 total tags in treatment: 13615384 INFO @ Tue, 16 Jun 2020 09:35:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:31: #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 09:35:31: #1 tags after filtering in treatment: 13615384 INFO @ Tue, 16 Jun 2020 09:35:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:32: #2 number of paired peaks: 246 WARNING @ Tue, 16 Jun 2020 09:35:32: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:32: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:35:32: #2 alternative fragment length(s) may be 2,45,566 bps INFO @ Tue, 16 Jun 2020 09:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:32: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:32: #2 You may need to consider one of the other alternative d(s): 2,45,566 WARNING @ Tue, 16 Jun 2020 09:35:32: #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 09:35:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:33: 10000000 INFO @ Tue, 16 Jun 2020 09:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:39: 11000000 INFO @ Tue, 16 Jun 2020 09:35:45: 12000000 INFO @ Tue, 16 Jun 2020 09:35:50: 13000000 INFO @ Tue, 16 Jun 2020 09:35:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:54: #1 total tags in treatment: 13615384 INFO @ Tue, 16 Jun 2020 09:35:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:54: #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 09:35:54: #1 tags after filtering in treatment: 13615384 INFO @ Tue, 16 Jun 2020 09:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:55: #2 number of paired peaks: 246 WARNING @ Tue, 16 Jun 2020 09:35:55: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:55: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:35:55: #2 alternative fragment length(s) may be 2,45,566 bps INFO @ Tue, 16 Jun 2020 09:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:55: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:55: #2 You may need to consider one of the other alternative d(s): 2,45,566 WARNING @ Tue, 16 Jun 2020 09:35:55: #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 09:35:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020832/SRX5020832.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 1 millis CompletedMACS2peakCalling