Job ID = 6368610 SRX = SRX5020835 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:46 prefetch.2.10.7: 1) Downloading 'SRR8201458'... 2020-06-16T00:28:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:08 prefetch.2.10.7: 'SRR8201458' is valid 2020-06-16T00:30:08 prefetch.2.10.7: 1) 'SRR8201458' was downloaded successfully 2020-06-16T00:30:08 prefetch.2.10.7: 'SRR8201458' has 0 unresolved dependencies Read 14214457 spots for SRR8201458/SRR8201458.sra Written 14214457 spots for SRR8201458/SRR8201458.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: 00:00:01 Multiseed full-index search: 00:03:20 14214457 reads; of these: 14214457 (100.00%) were unpaired; of these: 217729 (1.53%) aligned 0 times 11521293 (81.05%) aligned exactly 1 time 2475435 (17.41%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 1284874 / 13996728 = 0.0918 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 09:37:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.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 09:37:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:04: 1000000 INFO @ Tue, 16 Jun 2020 09:38:10: 2000000 INFO @ Tue, 16 Jun 2020 09:38:16: 3000000 INFO @ Tue, 16 Jun 2020 09:38:22: 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 09:38:28: 5000000 INFO @ Tue, 16 Jun 2020 09:38:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.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 09:38:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:34: 6000000 INFO @ Tue, 16 Jun 2020 09:38:34: 1000000 INFO @ Tue, 16 Jun 2020 09:38:40: 7000000 INFO @ Tue, 16 Jun 2020 09:38:40: 2000000 INFO @ Tue, 16 Jun 2020 09:38:46: 8000000 INFO @ Tue, 16 Jun 2020 09:38:47: 3000000 INFO @ Tue, 16 Jun 2020 09:38:52: 9000000 INFO @ Tue, 16 Jun 2020 09:38:53: 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 @ Tue, 16 Jun 2020 09:38:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.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 09:38:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:59: 10000000 INFO @ Tue, 16 Jun 2020 09:38:59: 5000000 INFO @ Tue, 16 Jun 2020 09:39:04: 1000000 INFO @ Tue, 16 Jun 2020 09:39:05: 11000000 INFO @ Tue, 16 Jun 2020 09:39:05: 6000000 INFO @ Tue, 16 Jun 2020 09:39:10: 2000000 INFO @ Tue, 16 Jun 2020 09:39:11: 12000000 INFO @ Tue, 16 Jun 2020 09:39:12: 7000000 INFO @ Tue, 16 Jun 2020 09:39:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:39:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:39:16: #1 total tags in treatment: 12711854 INFO @ Tue, 16 Jun 2020 09:39:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:16: #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 09:39:16: #1 tags after filtering in treatment: 12711854 INFO @ Tue, 16 Jun 2020 09:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:17: 3000000 INFO @ Tue, 16 Jun 2020 09:39:17: #2 number of paired peaks: 285 WARNING @ Tue, 16 Jun 2020 09:39:17: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:17: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:39:17: #2 alternative fragment length(s) may be 2,52,575 bps INFO @ Tue, 16 Jun 2020 09:39:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.05_model.r WARNING @ Tue, 16 Jun 2020 09:39:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:17: #2 You may need to consider one of the other alternative d(s): 2,52,575 WARNING @ Tue, 16 Jun 2020 09:39:17: #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 09:39:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:18: 8000000 INFO @ Tue, 16 Jun 2020 09:39:23: 4000000 INFO @ Tue, 16 Jun 2020 09:39:24: 9000000 INFO @ Tue, 16 Jun 2020 09:39:29: 5000000 INFO @ Tue, 16 Jun 2020 09:39:31: 10000000 INFO @ Tue, 16 Jun 2020 09:39:35: 6000000 INFO @ Tue, 16 Jun 2020 09:39:37: 11000000 INFO @ Tue, 16 Jun 2020 09:39:41: 7000000 INFO @ Tue, 16 Jun 2020 09:39:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:43: 12000000 INFO @ Tue, 16 Jun 2020 09:39:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:39:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:39:48: #1 total tags in treatment: 12711854 INFO @ Tue, 16 Jun 2020 09:39:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:48: #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 09:39:48: 8000000 INFO @ Tue, 16 Jun 2020 09:39:48: #1 tags after filtering in treatment: 12711854 INFO @ Tue, 16 Jun 2020 09:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:49: #2 number of paired peaks: 285 WARNING @ Tue, 16 Jun 2020 09:39:49: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:49: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:39:49: #2 alternative fragment length(s) may be 2,52,575 bps INFO @ Tue, 16 Jun 2020 09:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:49: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:49: #2 You may need to consider one of the other alternative d(s): 2,52,575 WARNING @ Tue, 16 Jun 2020 09:39:49: #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 09:39:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:54: 9000000 INFO @ Tue, 16 Jun 2020 09:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:00: 10000000 INFO @ Tue, 16 Jun 2020 09:40:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:12: 12000000 INFO @ Tue, 16 Jun 2020 09:40:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:16: #1 total tags in treatment: 12711854 INFO @ Tue, 16 Jun 2020 09:40:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:16: #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 09:40:16: #1 tags after filtering in treatment: 12711854 INFO @ Tue, 16 Jun 2020 09:40:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:17: #2 number of paired peaks: 285 WARNING @ Tue, 16 Jun 2020 09:40:17: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:17: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:40:17: #2 alternative fragment length(s) may be 2,52,575 bps INFO @ Tue, 16 Jun 2020 09:40:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:17: #2 You may need to consider one of the other alternative d(s): 2,52,575 WARNING @ Tue, 16 Jun 2020 09:40:17: #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 09:40:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020835/SRX5020835.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling