Job ID = 6368761 SRX = SRX5545246 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:12 prefetch.2.10.7: 1) Downloading 'SRR8754490'... 2020-06-16T00:31:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:33 prefetch.2.10.7: 1) 'SRR8754490' was downloaded successfully 2020-06-16T00:35:33 prefetch.2.10.7: 'SRR8754490' has 0 unresolved dependencies Read 43368755 spots for SRR8754490/SRR8754490.sra Written 43368755 spots for SRR8754490/SRR8754490.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: 00:07:47 43368755 reads; of these: 43368755 (100.00%) were unpaired; of these: 11420148 (26.33%) aligned 0 times 26869703 (61.96%) aligned exactly 1 time 5078904 (11.71%) aligned >1 times 73.67% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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 16 files... [bam_rmdupse_core] 9014220 / 31948607 = 0.2821 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 09:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.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 09:50:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:06: 1000000 INFO @ Tue, 16 Jun 2020 09:51:12: 2000000 INFO @ Tue, 16 Jun 2020 09:51:18: 3000000 INFO @ Tue, 16 Jun 2020 09:51:25: 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 09:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.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 09:51:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:31: 5000000 INFO @ Tue, 16 Jun 2020 09:51:36: 1000000 INFO @ Tue, 16 Jun 2020 09:51:38: 6000000 INFO @ Tue, 16 Jun 2020 09:51:43: 2000000 INFO @ Tue, 16 Jun 2020 09:51:45: 7000000 INFO @ Tue, 16 Jun 2020 09:51:49: 3000000 INFO @ Tue, 16 Jun 2020 09:51:52: 8000000 INFO @ Tue, 16 Jun 2020 09:51:56: 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 09:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.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 09:51:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:00: 9000000 INFO @ Tue, 16 Jun 2020 09:52:02: 5000000 INFO @ Tue, 16 Jun 2020 09:52:06: 1000000 INFO @ Tue, 16 Jun 2020 09:52:07: 10000000 INFO @ Tue, 16 Jun 2020 09:52:08: 6000000 INFO @ Tue, 16 Jun 2020 09:52:12: 2000000 INFO @ Tue, 16 Jun 2020 09:52:15: 11000000 INFO @ Tue, 16 Jun 2020 09:52:15: 7000000 INFO @ Tue, 16 Jun 2020 09:52:19: 3000000 INFO @ Tue, 16 Jun 2020 09:52:22: 8000000 INFO @ Tue, 16 Jun 2020 09:52:22: 12000000 INFO @ Tue, 16 Jun 2020 09:52:25: 4000000 INFO @ Tue, 16 Jun 2020 09:52:28: 9000000 INFO @ Tue, 16 Jun 2020 09:52:30: 13000000 INFO @ Tue, 16 Jun 2020 09:52:32: 5000000 INFO @ Tue, 16 Jun 2020 09:52:35: 10000000 INFO @ Tue, 16 Jun 2020 09:52:38: 14000000 INFO @ Tue, 16 Jun 2020 09:52:39: 6000000 INFO @ Tue, 16 Jun 2020 09:52:42: 11000000 INFO @ Tue, 16 Jun 2020 09:52:45: 15000000 INFO @ Tue, 16 Jun 2020 09:52:46: 7000000 INFO @ Tue, 16 Jun 2020 09:52:49: 12000000 INFO @ Tue, 16 Jun 2020 09:52:52: 8000000 INFO @ Tue, 16 Jun 2020 09:52:53: 16000000 INFO @ Tue, 16 Jun 2020 09:52:55: 13000000 INFO @ Tue, 16 Jun 2020 09:52:59: 9000000 INFO @ Tue, 16 Jun 2020 09:53:00: 17000000 INFO @ Tue, 16 Jun 2020 09:53:02: 14000000 INFO @ Tue, 16 Jun 2020 09:53:06: 10000000 INFO @ Tue, 16 Jun 2020 09:53:08: 18000000 INFO @ Tue, 16 Jun 2020 09:53:09: 15000000 INFO @ Tue, 16 Jun 2020 09:53:13: 11000000 INFO @ Tue, 16 Jun 2020 09:53:15: 19000000 INFO @ Tue, 16 Jun 2020 09:53:16: 16000000 INFO @ Tue, 16 Jun 2020 09:53:20: 12000000 INFO @ Tue, 16 Jun 2020 09:53:22: 20000000 INFO @ Tue, 16 Jun 2020 09:53:22: 17000000 INFO @ Tue, 16 Jun 2020 09:53:26: 13000000 INFO @ Tue, 16 Jun 2020 09:53:29: 18000000 INFO @ Tue, 16 Jun 2020 09:53:30: 21000000 INFO @ Tue, 16 Jun 2020 09:53:33: 14000000 INFO @ Tue, 16 Jun 2020 09:53:36: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:37: 22000000 INFO @ Tue, 16 Jun 2020 09:53:40: 15000000 INFO @ Tue, 16 Jun 2020 09:53:42: 20000000 INFO @ Tue, 16 Jun 2020 09:53:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:53:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:53:44: #1 total tags in treatment: 22934387 INFO @ Tue, 16 Jun 2020 09:53:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:44: #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 09:53:44: #1 tags after filtering in treatment: 22934387 INFO @ Tue, 16 Jun 2020 09:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:46: #2 number of paired peaks: 167 WARNING @ Tue, 16 Jun 2020 09:53:46: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:46: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:53:46: #2 alternative fragment length(s) may be 3,69 bps INFO @ Tue, 16 Jun 2020 09:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.05_model.r WARNING @ Tue, 16 Jun 2020 09:53:46: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:46: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Tue, 16 Jun 2020 09:53:46: #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 09:53:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:46: 16000000 INFO @ Tue, 16 Jun 2020 09:53:49: 21000000 INFO @ Tue, 16 Jun 2020 09:53:52: 17000000 INFO @ Tue, 16 Jun 2020 09:53:55: 22000000 INFO @ Tue, 16 Jun 2020 09:53:58: 18000000 INFO @ Tue, 16 Jun 2020 09:54:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:01: #1 total tags in treatment: 22934387 INFO @ Tue, 16 Jun 2020 09:54:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:01: #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 09:54:02: #1 tags after filtering in treatment: 22934387 INFO @ Tue, 16 Jun 2020 09:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:03: #2 number of paired peaks: 167 WARNING @ Tue, 16 Jun 2020 09:54:03: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:03: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:54:03: #2 alternative fragment length(s) may be 3,69 bps INFO @ Tue, 16 Jun 2020 09:54:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:03: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:03: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Tue, 16 Jun 2020 09:54:03: #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 09:54:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:04: 19000000 INFO @ Tue, 16 Jun 2020 09:54:10: 20000000 INFO @ Tue, 16 Jun 2020 09:54:16: 21000000 INFO @ Tue, 16 Jun 2020 09:54:21: 22000000 INFO @ Tue, 16 Jun 2020 09:54:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:27: #1 total tags in treatment: 22934387 INFO @ Tue, 16 Jun 2020 09:54:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:27: #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 09:54:27: #1 tags after filtering in treatment: 22934387 INFO @ Tue, 16 Jun 2020 09:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:28: #2 number of paired peaks: 167 WARNING @ Tue, 16 Jun 2020 09:54:28: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:28: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:54:28: #2 alternative fragment length(s) may be 3,69 bps INFO @ Tue, 16 Jun 2020 09:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.20_model.r WARNING @ Tue, 16 Jun 2020 09:54:29: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:29: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Tue, 16 Jun 2020 09:54:29: #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 09:54:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (932 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (607 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545246/SRX5545246.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (260 records, 4 fields): 2 millis CompletedMACS2peakCalling