Job ID = 14160569 SRX = SRX10399013 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26032717 spots for SRR14022401/SRR14022401.sra Written 26032717 spots for SRR14022401/SRR14022401.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160706 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:42 26032717 reads; of these: 26032717 (100.00%) were unpaired; of these: 5943295 (22.83%) aligned 0 times 16867648 (64.79%) aligned exactly 1 time 3221774 (12.38%) aligned >1 times 77.17% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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] 3212357 / 20089422 = 0.1599 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.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 @ Thu, 09 Dec 2021 03:27:24: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:27:24: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:27:32: 1000000 INFO @ Thu, 09 Dec 2021 03:27:39: 2000000 INFO @ Thu, 09 Dec 2021 03:27:47: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:27:54: 4000000 INFO @ Thu, 09 Dec 2021 03:27:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.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 @ Thu, 09 Dec 2021 03:27:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:27:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:02: 5000000 INFO @ Thu, 09 Dec 2021 03:28:02: 1000000 INFO @ Thu, 09 Dec 2021 03:28:11: 2000000 INFO @ Thu, 09 Dec 2021 03:28:11: 6000000 INFO @ Thu, 09 Dec 2021 03:28:19: 7000000 INFO @ Thu, 09 Dec 2021 03:28:19: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.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 @ Thu, 09 Dec 2021 03:28:22: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:28:22: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:28: 8000000 INFO @ Thu, 09 Dec 2021 03:28:28: 4000000 INFO @ Thu, 09 Dec 2021 03:28:31: 1000000 INFO @ Thu, 09 Dec 2021 03:28:37: 9000000 INFO @ Thu, 09 Dec 2021 03:28:37: 5000000 INFO @ Thu, 09 Dec 2021 03:28:40: 2000000 INFO @ Thu, 09 Dec 2021 03:28:45: 10000000 INFO @ Thu, 09 Dec 2021 03:28:46: 6000000 INFO @ Thu, 09 Dec 2021 03:28:48: 3000000 INFO @ Thu, 09 Dec 2021 03:28:53: 11000000 INFO @ Thu, 09 Dec 2021 03:28:54: 7000000 INFO @ Thu, 09 Dec 2021 03:28:57: 4000000 INFO @ Thu, 09 Dec 2021 03:29:02: 12000000 INFO @ Thu, 09 Dec 2021 03:29:03: 8000000 INFO @ Thu, 09 Dec 2021 03:29:05: 5000000 INFO @ Thu, 09 Dec 2021 03:29:10: 13000000 INFO @ Thu, 09 Dec 2021 03:29:11: 9000000 INFO @ Thu, 09 Dec 2021 03:29:14: 6000000 INFO @ Thu, 09 Dec 2021 03:29:18: 14000000 INFO @ Thu, 09 Dec 2021 03:29:20: 10000000 INFO @ Thu, 09 Dec 2021 03:29:22: 7000000 INFO @ Thu, 09 Dec 2021 03:29:26: 15000000 INFO @ Thu, 09 Dec 2021 03:29:28: 11000000 INFO @ Thu, 09 Dec 2021 03:29:31: 8000000 INFO @ Thu, 09 Dec 2021 03:29:35: 16000000 INFO @ Thu, 09 Dec 2021 03:29:36: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:29:39: 9000000 INFO @ Thu, 09 Dec 2021 03:29:42: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:29:42: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:29:42: #1 total tags in treatment: 16877065 INFO @ Thu, 09 Dec 2021 03:29:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:29:42: #1 tags after filtering in treatment: 16877065 INFO @ Thu, 09 Dec 2021 03:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:29:42: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:43: #2 number of paired peaks: 349 WARNING @ Thu, 09 Dec 2021 03:29:43: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Thu, 09 Dec 2021 03:29:43: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:43: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:44: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:44: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:44: #2 predicted fragment length is 109 bps INFO @ Thu, 09 Dec 2021 03:29:44: #2 alternative fragment length(s) may be 4,109 bps INFO @ Thu, 09 Dec 2021 03:29:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.05_model.r WARNING @ Thu, 09 Dec 2021 03:29:44: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:29:44: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Thu, 09 Dec 2021 03:29:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:29:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:45: 13000000 INFO @ Thu, 09 Dec 2021 03:29:48: 10000000 INFO @ Thu, 09 Dec 2021 03:29:53: 14000000 INFO @ Thu, 09 Dec 2021 03:29:56: 11000000 INFO @ Thu, 09 Dec 2021 03:30:02: 15000000 INFO @ Thu, 09 Dec 2021 03:30:04: 12000000 INFO @ Thu, 09 Dec 2021 03:30:10: 16000000 INFO @ Thu, 09 Dec 2021 03:30:13: 13000000 INFO @ Thu, 09 Dec 2021 03:30:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:30:17: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:30:17: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:30:17: #1 total tags in treatment: 16877065 INFO @ Thu, 09 Dec 2021 03:30:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:30:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:30:17: #1 tags after filtering in treatment: 16877065 INFO @ Thu, 09 Dec 2021 03:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:30:17: #1 finished! INFO @ Thu, 09 Dec 2021 03:30:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:30:19: #2 number of paired peaks: 349 WARNING @ Thu, 09 Dec 2021 03:30:19: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Thu, 09 Dec 2021 03:30:19: start model_add_line... INFO @ Thu, 09 Dec 2021 03:30:19: start X-correlation... INFO @ Thu, 09 Dec 2021 03:30:19: end of X-cor INFO @ Thu, 09 Dec 2021 03:30:19: #2 finished! INFO @ Thu, 09 Dec 2021 03:30:19: #2 predicted fragment length is 109 bps INFO @ Thu, 09 Dec 2021 03:30:19: #2 alternative fragment length(s) may be 4,109 bps INFO @ Thu, 09 Dec 2021 03:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.10_model.r WARNING @ Thu, 09 Dec 2021 03:30:19: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:30:19: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Thu, 09 Dec 2021 03:30:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:30:19: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:30:20: 14000000 INFO @ Thu, 09 Dec 2021 03:30:28: 15000000 INFO @ Thu, 09 Dec 2021 03:30:35: 16000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:30:42: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:30:42: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:30:42: #1 total tags in treatment: 16877065 INFO @ Thu, 09 Dec 2021 03:30:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:30:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:30:42: #1 tags after filtering in treatment: 16877065 INFO @ Thu, 09 Dec 2021 03:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:30:42: #1 finished! INFO @ Thu, 09 Dec 2021 03:30:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:30:43: #2 number of paired peaks: 349 WARNING @ Thu, 09 Dec 2021 03:30:43: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Thu, 09 Dec 2021 03:30:43: start model_add_line... INFO @ Thu, 09 Dec 2021 03:30:43: start X-correlation... INFO @ Thu, 09 Dec 2021 03:30:43: end of X-cor INFO @ Thu, 09 Dec 2021 03:30:43: #2 finished! INFO @ Thu, 09 Dec 2021 03:30:43: #2 predicted fragment length is 109 bps INFO @ Thu, 09 Dec 2021 03:30:43: #2 alternative fragment length(s) may be 4,109 bps INFO @ Thu, 09 Dec 2021 03:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.20_model.r WARNING @ Thu, 09 Dec 2021 03:30:43: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:30:43: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Thu, 09 Dec 2021 03:30:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:30:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:30:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.05_summits.bed INFO @ Thu, 09 Dec 2021 03:30:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2176 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.10_summits.bed INFO @ Thu, 09 Dec 2021 03:31:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1393 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:31:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:31:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:31:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:31:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399013/SRX10399013.20_summits.bed INFO @ Thu, 09 Dec 2021 03:31:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (836 records, 4 fields): 3 millis CompletedMACS2peakCalling