Job ID = 10165772 SRX = SRX9120608 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27560836 spots for SRR12638551/SRR12638551.sra Written 27560836 spots for SRR12638551/SRR12638551.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166073 ("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: 00:06:10 27560836 reads; of these: 27560836 (100.00%) were unpaired; of these: 1658099 (6.02%) aligned 0 times 21456775 (77.85%) aligned exactly 1 time 4445962 (16.13%) aligned >1 times 93.98% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 4399494 / 25902737 = 0.1698 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 @ Thu, 08 Oct 2020 20:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.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, 08 Oct 2020 20:01:40: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:01:40: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:01:46: 1000000 INFO @ Thu, 08 Oct 2020 20:01:51: 2000000 INFO @ Thu, 08 Oct 2020 20:01:56: 3000000 INFO @ Thu, 08 Oct 2020 20:02:02: 4000000 INFO @ Thu, 08 Oct 2020 20:02:07: 5000000 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 @ Thu, 08 Oct 2020 20:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.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, 08 Oct 2020 20:02:10: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:02:10: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:02:12: 6000000 INFO @ Thu, 08 Oct 2020 20:02:16: 1000000 INFO @ Thu, 08 Oct 2020 20:02:17: 7000000 INFO @ Thu, 08 Oct 2020 20:02:22: 2000000 INFO @ Thu, 08 Oct 2020 20:02:23: 8000000 INFO @ Thu, 08 Oct 2020 20:02:28: 3000000 INFO @ Thu, 08 Oct 2020 20:02:29: 9000000 INFO @ Thu, 08 Oct 2020 20:02:34: 4000000 INFO @ Thu, 08 Oct 2020 20:02:34: 10000000 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 @ Thu, 08 Oct 2020 20:02:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.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, 08 Oct 2020 20:02:40: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:02:40: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:02:40: 11000000 INFO @ Thu, 08 Oct 2020 20:02:40: 5000000 INFO @ Thu, 08 Oct 2020 20:02:46: 12000000 INFO @ Thu, 08 Oct 2020 20:02:46: 1000000 INFO @ Thu, 08 Oct 2020 20:02:46: 6000000 INFO @ Thu, 08 Oct 2020 20:02:51: 13000000 INFO @ Thu, 08 Oct 2020 20:02:53: 2000000 INFO @ Thu, 08 Oct 2020 20:02:53: 7000000 INFO @ Thu, 08 Oct 2020 20:02:57: 14000000 INFO @ Thu, 08 Oct 2020 20:02:59: 3000000 INFO @ Thu, 08 Oct 2020 20:02:59: 8000000 INFO @ Thu, 08 Oct 2020 20:03:03: 15000000 INFO @ Thu, 08 Oct 2020 20:03:05: 4000000 INFO @ Thu, 08 Oct 2020 20:03:06: 9000000 INFO @ Thu, 08 Oct 2020 20:03:09: 16000000 INFO @ Thu, 08 Oct 2020 20:03:12: 5000000 INFO @ Thu, 08 Oct 2020 20:03:12: 10000000 INFO @ Thu, 08 Oct 2020 20:03:15: 17000000 INFO @ Thu, 08 Oct 2020 20:03:18: 6000000 INFO @ Thu, 08 Oct 2020 20:03:18: 11000000 INFO @ Thu, 08 Oct 2020 20:03:21: 18000000 INFO @ Thu, 08 Oct 2020 20:03:24: 7000000 INFO @ Thu, 08 Oct 2020 20:03:25: 12000000 INFO @ Thu, 08 Oct 2020 20:03:26: 19000000 INFO @ Thu, 08 Oct 2020 20:03:30: 8000000 INFO @ Thu, 08 Oct 2020 20:03:31: 13000000 INFO @ Thu, 08 Oct 2020 20:03:32: 20000000 INFO @ Thu, 08 Oct 2020 20:03:37: 9000000 INFO @ Thu, 08 Oct 2020 20:03:37: 14000000 INFO @ Thu, 08 Oct 2020 20:03:39: 21000000 INFO @ Thu, 08 Oct 2020 20:03:42: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:03:42: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:03:42: #1 total tags in treatment: 21503243 INFO @ Thu, 08 Oct 2020 20:03:42: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:03:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:03:42: #1 tags after filtering in treatment: 21503243 INFO @ Thu, 08 Oct 2020 20:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:03:42: #1 finished! INFO @ Thu, 08 Oct 2020 20:03:42: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:03:43: 10000000 INFO @ Thu, 08 Oct 2020 20:03:43: 15000000 INFO @ Thu, 08 Oct 2020 20:03:43: #2 number of paired peaks: 204 WARNING @ Thu, 08 Oct 2020 20:03:43: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Thu, 08 Oct 2020 20:03:43: start model_add_line... INFO @ Thu, 08 Oct 2020 20:03:44: start X-correlation... INFO @ Thu, 08 Oct 2020 20:03:44: end of X-cor INFO @ Thu, 08 Oct 2020 20:03:44: #2 finished! INFO @ Thu, 08 Oct 2020 20:03:44: #2 predicted fragment length is 49 bps INFO @ Thu, 08 Oct 2020 20:03:44: #2 alternative fragment length(s) may be 1,49,504 bps INFO @ Thu, 08 Oct 2020 20:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.05_model.r WARNING @ Thu, 08 Oct 2020 20:03:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:03:44: #2 You may need to consider one of the other alternative d(s): 1,49,504 WARNING @ Thu, 08 Oct 2020 20:03:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:03:44: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:03:49: 11000000 INFO @ Thu, 08 Oct 2020 20:03:50: 16000000 INFO @ Thu, 08 Oct 2020 20:03:56: 12000000 INFO @ Thu, 08 Oct 2020 20:03:56: 17000000 INFO @ Thu, 08 Oct 2020 20:04:02: 13000000 INFO @ Thu, 08 Oct 2020 20:04:02: 18000000 INFO @ Thu, 08 Oct 2020 20:04:08: 14000000 INFO @ Thu, 08 Oct 2020 20:04:09: 19000000 INFO @ Thu, 08 Oct 2020 20:04:14: 15000000 INFO @ Thu, 08 Oct 2020 20:04:15: 20000000 INFO @ Thu, 08 Oct 2020 20:04:20: 16000000 INFO @ Thu, 08 Oct 2020 20:04:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:04:21: 21000000 INFO @ Thu, 08 Oct 2020 20:04:24: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:04:24: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:04:24: #1 total tags in treatment: 21503243 INFO @ Thu, 08 Oct 2020 20:04:24: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:04:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:04:25: #1 tags after filtering in treatment: 21503243 INFO @ Thu, 08 Oct 2020 20:04:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:04:25: #1 finished! INFO @ Thu, 08 Oct 2020 20:04:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:04:26: #2 number of paired peaks: 204 WARNING @ Thu, 08 Oct 2020 20:04:26: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Thu, 08 Oct 2020 20:04:26: start model_add_line... INFO @ Thu, 08 Oct 2020 20:04:26: start X-correlation... INFO @ Thu, 08 Oct 2020 20:04:26: end of X-cor INFO @ Thu, 08 Oct 2020 20:04:26: #2 finished! INFO @ Thu, 08 Oct 2020 20:04:26: #2 predicted fragment length is 49 bps INFO @ Thu, 08 Oct 2020 20:04:26: #2 alternative fragment length(s) may be 1,49,504 bps INFO @ Thu, 08 Oct 2020 20:04:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.10_model.r WARNING @ Thu, 08 Oct 2020 20:04:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:04:26: #2 You may need to consider one of the other alternative d(s): 1,49,504 WARNING @ Thu, 08 Oct 2020 20:04:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:04:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:04:26: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:04:32: 18000000 INFO @ Thu, 08 Oct 2020 20:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.05_summits.bed INFO @ Thu, 08 Oct 2020 20:04:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (743 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:04:38: 19000000 INFO @ Thu, 08 Oct 2020 20:04:44: 20000000 INFO @ Thu, 08 Oct 2020 20:04:50: 21000000 INFO @ Thu, 08 Oct 2020 20:04:53: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:04:53: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:04:53: #1 total tags in treatment: 21503243 INFO @ Thu, 08 Oct 2020 20:04:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:04:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:04:54: #1 tags after filtering in treatment: 21503243 INFO @ Thu, 08 Oct 2020 20:04:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:04:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:04:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:04:55: #2 number of paired peaks: 204 WARNING @ Thu, 08 Oct 2020 20:04:55: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Thu, 08 Oct 2020 20:04:55: start model_add_line... INFO @ Thu, 08 Oct 2020 20:04:55: start X-correlation... INFO @ Thu, 08 Oct 2020 20:04:55: end of X-cor INFO @ Thu, 08 Oct 2020 20:04:55: #2 finished! INFO @ Thu, 08 Oct 2020 20:04:55: #2 predicted fragment length is 49 bps INFO @ Thu, 08 Oct 2020 20:04:55: #2 alternative fragment length(s) may be 1,49,504 bps INFO @ Thu, 08 Oct 2020 20:04:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.20_model.r WARNING @ Thu, 08 Oct 2020 20:04:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:04:55: #2 You may need to consider one of the other alternative d(s): 1,49,504 WARNING @ Thu, 08 Oct 2020 20:04:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:04:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:04:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:05:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.10_summits.bed INFO @ Thu, 08 Oct 2020 20:05:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:05:32: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120608/SRX9120608.20_summits.bed INFO @ Thu, 08 Oct 2020 20:05:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling