Job ID = 10165791 SRX = SRX9120620 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23786791 spots for SRR12638563/SRR12638563.sra Written 23786791 spots for SRR12638563/SRR12638563.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166096 ("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: 00:04:59 23786791 reads; of these: 23786791 (100.00%) were unpaired; of these: 115043 (0.48%) aligned 0 times 19854069 (83.47%) aligned exactly 1 time 3817679 (16.05%) aligned >1 times 99.52% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 3688099 / 23671748 = 0.1558 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 20:03:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.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 20:03:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:03:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:03:46: 1000000 INFO @ Thu, 08 Oct 2020 20:03:53: 2000000 INFO @ Thu, 08 Oct 2020 20:04:00: 3000000 INFO @ Thu, 08 Oct 2020 20:04:07: 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 @ Thu, 08 Oct 2020 20:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.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 20:04:10: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:10: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:13: 5000000 INFO @ Thu, 08 Oct 2020 20:04:17: 1000000 INFO @ Thu, 08 Oct 2020 20:04:21: 6000000 INFO @ Thu, 08 Oct 2020 20:04:24: 2000000 INFO @ Thu, 08 Oct 2020 20:04:28: 7000000 INFO @ Thu, 08 Oct 2020 20:04:31: 3000000 INFO @ Thu, 08 Oct 2020 20:04:35: 8000000 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 20:04:38: 4000000 INFO @ Thu, 08 Oct 2020 20:04:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.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 20:04:41: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:41: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:42: 9000000 INFO @ Thu, 08 Oct 2020 20:04:45: 5000000 INFO @ Thu, 08 Oct 2020 20:04:48: 1000000 INFO @ Thu, 08 Oct 2020 20:04:49: 10000000 INFO @ Thu, 08 Oct 2020 20:04:52: 6000000 INFO @ Thu, 08 Oct 2020 20:04:55: 2000000 INFO @ Thu, 08 Oct 2020 20:04:57: 11000000 INFO @ Thu, 08 Oct 2020 20:04:59: 7000000 INFO @ Thu, 08 Oct 2020 20:05:03: 3000000 INFO @ Thu, 08 Oct 2020 20:05:04: 12000000 INFO @ Thu, 08 Oct 2020 20:05:07: 8000000 INFO @ Thu, 08 Oct 2020 20:05:10: 4000000 INFO @ Thu, 08 Oct 2020 20:05:11: 13000000 INFO @ Thu, 08 Oct 2020 20:05:14: 9000000 INFO @ Thu, 08 Oct 2020 20:05:17: 5000000 INFO @ Thu, 08 Oct 2020 20:05:18: 14000000 INFO @ Thu, 08 Oct 2020 20:05:21: 10000000 INFO @ Thu, 08 Oct 2020 20:05:25: 6000000 INFO @ Thu, 08 Oct 2020 20:05:25: 15000000 INFO @ Thu, 08 Oct 2020 20:05:28: 11000000 INFO @ Thu, 08 Oct 2020 20:05:32: 7000000 INFO @ Thu, 08 Oct 2020 20:05:32: 16000000 INFO @ Thu, 08 Oct 2020 20:05:35: 12000000 INFO @ Thu, 08 Oct 2020 20:05:39: 8000000 INFO @ Thu, 08 Oct 2020 20:05:40: 17000000 INFO @ Thu, 08 Oct 2020 20:05:43: 13000000 INFO @ Thu, 08 Oct 2020 20:05:46: 9000000 INFO @ Thu, 08 Oct 2020 20:05:47: 18000000 INFO @ Thu, 08 Oct 2020 20:05:50: 14000000 INFO @ Thu, 08 Oct 2020 20:05:53: 10000000 INFO @ Thu, 08 Oct 2020 20:05:54: 19000000 INFO @ Thu, 08 Oct 2020 20:05:57: 15000000 INFO @ Thu, 08 Oct 2020 20:06:01: 11000000 INFO @ Thu, 08 Oct 2020 20:06:01: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:01: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:01: #1 total tags in treatment: 19983649 INFO @ Thu, 08 Oct 2020 20:06:01: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:01: #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 20:06:02: #1 tags after filtering in treatment: 19983649 INFO @ Thu, 08 Oct 2020 20:06:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:02: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:02: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:03: #2 number of paired peaks: 184 WARNING @ Thu, 08 Oct 2020 20:06:03: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:03: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:03: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:03: #2 alternative fragment length(s) may be 1,48,532,557 bps INFO @ Thu, 08 Oct 2020 20:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.05_model.r WARNING @ Thu, 08 Oct 2020 20:06:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:03: #2 You may need to consider one of the other alternative d(s): 1,48,532,557 WARNING @ Thu, 08 Oct 2020 20:06:03: #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 20:06:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:04: 16000000 INFO @ Thu, 08 Oct 2020 20:06:08: 12000000 INFO @ Thu, 08 Oct 2020 20:06:11: 17000000 INFO @ Thu, 08 Oct 2020 20:06:15: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:06:19: 18000000 INFO @ Thu, 08 Oct 2020 20:06:21: 14000000 INFO @ Thu, 08 Oct 2020 20:06:26: 19000000 INFO @ Thu, 08 Oct 2020 20:06:27: 15000000 INFO @ Thu, 08 Oct 2020 20:06:33: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:33: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:33: #1 total tags in treatment: 19983649 INFO @ Thu, 08 Oct 2020 20:06:33: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:33: #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 20:06:33: #1 tags after filtering in treatment: 19983649 INFO @ Thu, 08 Oct 2020 20:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:33: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:33: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:34: #2 number of paired peaks: 184 WARNING @ Thu, 08 Oct 2020 20:06:34: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:34: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:34: 16000000 INFO @ Thu, 08 Oct 2020 20:06:34: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:34: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:34: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:34: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:34: #2 alternative fragment length(s) may be 1,48,532,557 bps INFO @ Thu, 08 Oct 2020 20:06:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.10_model.r WARNING @ Thu, 08 Oct 2020 20:06:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:34: #2 You may need to consider one of the other alternative d(s): 1,48,532,557 WARNING @ Thu, 08 Oct 2020 20:06:34: #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 20:06:34: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:39: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:41: 17000000 INFO @ Thu, 08 Oct 2020 20:06:48: 18000000 INFO @ Thu, 08 Oct 2020 20:06:54: 19000000 INFO @ Thu, 08 Oct 2020 20:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.05_summits.bed INFO @ Thu, 08 Oct 2020 20:06:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:01: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:01: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:01: #1 total tags in treatment: 19983649 INFO @ Thu, 08 Oct 2020 20:07:01: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:01: #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 20:07:01: #1 tags after filtering in treatment: 19983649 INFO @ Thu, 08 Oct 2020 20:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:01: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:01: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:02: #2 number of paired peaks: 184 WARNING @ Thu, 08 Oct 2020 20:07:02: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:02: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:03: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:03: #2 alternative fragment length(s) may be 1,48,532,557 bps INFO @ Thu, 08 Oct 2020 20:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.20_model.r WARNING @ Thu, 08 Oct 2020 20:07:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:07:03: #2 You may need to consider one of the other alternative d(s): 1,48,532,557 WARNING @ Thu, 08 Oct 2020 20:07:03: #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 20:07:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:07:10: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.10_summits.bed INFO @ Thu, 08 Oct 2020 20:07:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120620/SRX9120620.20_summits.bed INFO @ Thu, 08 Oct 2020 20:07:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling