Job ID = 6368576 SRX = SRX5020802 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:01 prefetch.2.10.7: 1) Downloading 'SRR8201425'... 2020-06-16T00:27:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:07 prefetch.2.10.7: 1) 'SRR8201425' was downloaded successfully 2020-06-16T00:30:07 prefetch.2.10.7: 'SRR8201425' has 0 unresolved dependencies Read 27682668 spots for SRR8201425/SRR8201425.sra Written 27682668 spots for SRR8201425/SRR8201425.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: 00:09:24 27682668 reads; of these: 27682668 (100.00%) were unpaired; of these: 816555 (2.95%) aligned 0 times 22350584 (80.74%) aligned exactly 1 time 4515529 (16.31%) aligned >1 times 97.05% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 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 12 files... [bam_rmdupse_core] 4401883 / 26866113 = 0.1638 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 09:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.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 09:48:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:07: 1000000 INFO @ Tue, 16 Jun 2020 09:48:13: 2000000 INFO @ Tue, 16 Jun 2020 09:48:20: 3000000 INFO @ Tue, 16 Jun 2020 09:48:27: 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 09:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.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 09:48:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:34: 5000000 INFO @ Tue, 16 Jun 2020 09:48:37: 1000000 INFO @ Tue, 16 Jun 2020 09:48:41: 6000000 INFO @ Tue, 16 Jun 2020 09:48:43: 2000000 INFO @ Tue, 16 Jun 2020 09:48:48: 7000000 INFO @ Tue, 16 Jun 2020 09:48:50: 3000000 INFO @ Tue, 16 Jun 2020 09:48:55: 8000000 INFO @ Tue, 16 Jun 2020 09:48:57: 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 09:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.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 09:49:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:02: 9000000 INFO @ Tue, 16 Jun 2020 09:49:04: 5000000 INFO @ Tue, 16 Jun 2020 09:49:07: 1000000 INFO @ Tue, 16 Jun 2020 09:49:09: 10000000 INFO @ Tue, 16 Jun 2020 09:49:10: 6000000 INFO @ Tue, 16 Jun 2020 09:49:13: 2000000 INFO @ Tue, 16 Jun 2020 09:49:17: 7000000 INFO @ Tue, 16 Jun 2020 09:49:17: 11000000 INFO @ Tue, 16 Jun 2020 09:49:20: 3000000 INFO @ Tue, 16 Jun 2020 09:49:23: 8000000 INFO @ Tue, 16 Jun 2020 09:49:24: 12000000 INFO @ Tue, 16 Jun 2020 09:49:27: 4000000 INFO @ Tue, 16 Jun 2020 09:49:30: 9000000 INFO @ Tue, 16 Jun 2020 09:49:31: 13000000 INFO @ Tue, 16 Jun 2020 09:49:33: 5000000 INFO @ Tue, 16 Jun 2020 09:49:37: 10000000 INFO @ Tue, 16 Jun 2020 09:49:38: 14000000 INFO @ Tue, 16 Jun 2020 09:49:40: 6000000 INFO @ Tue, 16 Jun 2020 09:49:43: 11000000 INFO @ Tue, 16 Jun 2020 09:49:45: 15000000 INFO @ Tue, 16 Jun 2020 09:49:46: 7000000 INFO @ Tue, 16 Jun 2020 09:49:50: 12000000 INFO @ Tue, 16 Jun 2020 09:49:52: 16000000 INFO @ Tue, 16 Jun 2020 09:49:53: 8000000 INFO @ Tue, 16 Jun 2020 09:49:56: 13000000 INFO @ Tue, 16 Jun 2020 09:49:59: 17000000 INFO @ Tue, 16 Jun 2020 09:49:59: 9000000 INFO @ Tue, 16 Jun 2020 09:50:03: 14000000 INFO @ Tue, 16 Jun 2020 09:50:06: 10000000 INFO @ Tue, 16 Jun 2020 09:50:06: 18000000 INFO @ Tue, 16 Jun 2020 09:50:09: 15000000 INFO @ Tue, 16 Jun 2020 09:50:12: 11000000 INFO @ Tue, 16 Jun 2020 09:50:13: 19000000 INFO @ Tue, 16 Jun 2020 09:50:15: 16000000 INFO @ Tue, 16 Jun 2020 09:50:18: 12000000 INFO @ Tue, 16 Jun 2020 09:50:19: 20000000 INFO @ Tue, 16 Jun 2020 09:50:21: 17000000 INFO @ Tue, 16 Jun 2020 09:50:25: 13000000 INFO @ Tue, 16 Jun 2020 09:50:26: 21000000 INFO @ Tue, 16 Jun 2020 09:50:28: 18000000 INFO @ Tue, 16 Jun 2020 09:50:31: 14000000 INFO @ Tue, 16 Jun 2020 09:50:33: 22000000 INFO @ Tue, 16 Jun 2020 09:50:34: 19000000 INFO @ Tue, 16 Jun 2020 09:50:37: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:37: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:37: #1 total tags in treatment: 22464230 INFO @ Tue, 16 Jun 2020 09:50:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:37: #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 09:50:37: #1 tags after filtering in treatment: 22464230 INFO @ Tue, 16 Jun 2020 09:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:37: 15000000 INFO @ Tue, 16 Jun 2020 09:50:38: #2 number of paired peaks: 177 WARNING @ Tue, 16 Jun 2020 09:50:38: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:39: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:50:39: #2 alternative fragment length(s) may be 1,74 bps INFO @ Tue, 16 Jun 2020 09:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.05_model.r WARNING @ Tue, 16 Jun 2020 09:50:39: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:39: #2 You may need to consider one of the other alternative d(s): 1,74 WARNING @ Tue, 16 Jun 2020 09:50:39: #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 09:50:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:40: 20000000 INFO @ Tue, 16 Jun 2020 09:50:43: 16000000 INFO @ Tue, 16 Jun 2020 09:50:46: 21000000 INFO @ Tue, 16 Jun 2020 09:50:49: 17000000 INFO @ Tue, 16 Jun 2020 09:50:52: 22000000 INFO @ Tue, 16 Jun 2020 09:50:55: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:55: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:55: #1 total tags in treatment: 22464230 INFO @ Tue, 16 Jun 2020 09:50:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:55: #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 09:50:55: #1 tags after filtering in treatment: 22464230 INFO @ Tue, 16 Jun 2020 09:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:56: 18000000 INFO @ Tue, 16 Jun 2020 09:50:57: #2 number of paired peaks: 177 WARNING @ Tue, 16 Jun 2020 09:50:57: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:57: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:50:57: #2 alternative fragment length(s) may be 1,74 bps INFO @ Tue, 16 Jun 2020 09:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:57: #2 You may need to consider one of the other alternative d(s): 1,74 WARNING @ Tue, 16 Jun 2020 09:50:57: #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 09:50:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:01: 19000000 INFO @ Tue, 16 Jun 2020 09:51:07: 20000000 INFO @ Tue, 16 Jun 2020 09:51:13: 21000000 INFO @ Tue, 16 Jun 2020 09:51:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:19: 22000000 INFO @ Tue, 16 Jun 2020 09:51:21: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:21: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:21: #1 total tags in treatment: 22464230 INFO @ Tue, 16 Jun 2020 09:51:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:21: #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 09:51:22: #1 tags after filtering in treatment: 22464230 INFO @ Tue, 16 Jun 2020 09:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:23: #2 number of paired peaks: 177 WARNING @ Tue, 16 Jun 2020 09:51:23: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:23: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:51:23: #2 alternative fragment length(s) may be 1,74 bps INFO @ Tue, 16 Jun 2020 09:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:23: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:23: #2 You may need to consider one of the other alternative d(s): 1,74 WARNING @ Tue, 16 Jun 2020 09:51:23: #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 09:51:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (744 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020802/SRX5020802.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling