Job ID = 6368530 SRX = SRX5020759 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:38:01 prefetch.2.10.7: 1) Downloading 'SRR8201382'... 2020-06-16T00:38:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:39 prefetch.2.10.7: 1) 'SRR8201382' was downloaded successfully 2020-06-16T00:41:39 prefetch.2.10.7: 'SRR8201382' has 0 unresolved dependencies Read 33697049 spots for SRR8201382/SRR8201382.sra Written 33697049 spots for SRR8201382/SRR8201382.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: 00:07:14 33697049 reads; of these: 33697049 (100.00%) were unpaired; of these: 17246200 (51.18%) aligned 0 times 13568083 (40.26%) aligned exactly 1 time 2882766 (8.55%) aligned >1 times 48.82% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 3229672 / 16450849 = 0.1963 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 09:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.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 09:56:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:02: 1000000 INFO @ Tue, 16 Jun 2020 09:57:08: 2000000 INFO @ Tue, 16 Jun 2020 09:57:14: 3000000 INFO @ Tue, 16 Jun 2020 09:57:19: 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 09:57:25: 5000000 INFO @ Tue, 16 Jun 2020 09:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.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 09:57:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:31: 6000000 INFO @ Tue, 16 Jun 2020 09:57:33: 1000000 INFO @ Tue, 16 Jun 2020 09:57:37: 7000000 INFO @ Tue, 16 Jun 2020 09:57:40: 2000000 INFO @ Tue, 16 Jun 2020 09:57:44: 8000000 INFO @ Tue, 16 Jun 2020 09:57:47: 3000000 INFO @ Tue, 16 Jun 2020 09:57:50: 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 09:57:54: 4000000 INFO @ Tue, 16 Jun 2020 09:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.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 09:57:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:56: 10000000 INFO @ Tue, 16 Jun 2020 09:58:01: 5000000 INFO @ Tue, 16 Jun 2020 09:58:03: 1000000 INFO @ Tue, 16 Jun 2020 09:58:03: 11000000 INFO @ Tue, 16 Jun 2020 09:58:07: 6000000 INFO @ Tue, 16 Jun 2020 09:58:09: 2000000 INFO @ Tue, 16 Jun 2020 09:58:10: 12000000 INFO @ Tue, 16 Jun 2020 09:58:13: 7000000 INFO @ Tue, 16 Jun 2020 09:58:16: 3000000 INFO @ Tue, 16 Jun 2020 09:58:17: 13000000 INFO @ Tue, 16 Jun 2020 09:58:18: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:58:18: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:58:18: #1 total tags in treatment: 13221177 INFO @ Tue, 16 Jun 2020 09:58:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:18: #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 09:58:18: #1 tags after filtering in treatment: 13221177 INFO @ Tue, 16 Jun 2020 09:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:19: #2 number of paired peaks: 420 WARNING @ Tue, 16 Jun 2020 09:58:19: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 16 Jun 2020 09:58:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:19: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:58:19: #2 alternative fragment length(s) may be 95,598 bps INFO @ Tue, 16 Jun 2020 09:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.05_model.r WARNING @ Tue, 16 Jun 2020 09:58:19: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:58:19: #2 You may need to consider one of the other alternative d(s): 95,598 WARNING @ Tue, 16 Jun 2020 09:58:19: #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 09:58:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:20: 8000000 INFO @ Tue, 16 Jun 2020 09:58:22: 4000000 INFO @ Tue, 16 Jun 2020 09:58:28: 9000000 INFO @ Tue, 16 Jun 2020 09:58:28: 5000000 INFO @ Tue, 16 Jun 2020 09:58:35: 6000000 INFO @ Tue, 16 Jun 2020 09:58:36: 10000000 INFO @ Tue, 16 Jun 2020 09:58:41: 7000000 INFO @ Tue, 16 Jun 2020 09:58:43: 11000000 INFO @ Tue, 16 Jun 2020 09:58:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:48: 8000000 INFO @ Tue, 16 Jun 2020 09:58:51: 12000000 INFO @ Tue, 16 Jun 2020 09:58:54: 9000000 INFO @ Tue, 16 Jun 2020 09:58:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.05_summits.bed INFO @ Tue, 16 Jun 2020 09:58:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1471 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:58: 13000000 INFO @ Tue, 16 Jun 2020 09:58:59: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:58:59: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:58:59: #1 total tags in treatment: 13221177 INFO @ Tue, 16 Jun 2020 09:58:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:59: #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 09:59:00: #1 tags after filtering in treatment: 13221177 INFO @ Tue, 16 Jun 2020 09:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:00: 10000000 INFO @ Tue, 16 Jun 2020 09:59:01: #2 number of paired peaks: 420 WARNING @ Tue, 16 Jun 2020 09:59:01: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:01: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:59:01: #2 alternative fragment length(s) may be 95,598 bps INFO @ Tue, 16 Jun 2020 09:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.10_model.r WARNING @ Tue, 16 Jun 2020 09:59:01: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:59:01: #2 You may need to consider one of the other alternative d(s): 95,598 WARNING @ Tue, 16 Jun 2020 09:59:01: #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 09:59:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:06: 11000000 INFO @ Tue, 16 Jun 2020 09:59:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:59:18: 13000000 INFO @ Tue, 16 Jun 2020 09:59:20: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:59:20: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:59:20: #1 total tags in treatment: 13221177 INFO @ Tue, 16 Jun 2020 09:59:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:20: #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 09:59:20: #1 tags after filtering in treatment: 13221177 INFO @ Tue, 16 Jun 2020 09:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:21: #2 number of paired peaks: 420 WARNING @ Tue, 16 Jun 2020 09:59:21: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 16 Jun 2020 09:59:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:21: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:59:21: #2 alternative fragment length(s) may be 95,598 bps INFO @ Tue, 16 Jun 2020 09:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.20_model.r WARNING @ Tue, 16 Jun 2020 09:59:21: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:59:21: #2 You may need to consider one of the other alternative d(s): 95,598 WARNING @ Tue, 16 Jun 2020 09:59:21: #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 09:59:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.10_summits.bed INFO @ Tue, 16 Jun 2020 09:59:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (869 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:59:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020759/SRX5020759.20_summits.bed INFO @ Tue, 16 Jun 2020 09:59:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (497 records, 4 fields): 2 millis CompletedMACS2peakCalling