Job ID = 10165675 SRX = SRX8331152 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 87376107 spots for SRR11778465/SRR11778465.sra Written 87376107 spots for SRR11778465/SRR11778465.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166203 ("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: 00:31:30 87376107 reads; of these: 87376107 (100.00%) were unpaired; of these: 863661 (0.99%) aligned 0 times 73134011 (83.70%) aligned exactly 1 time 13378435 (15.31%) aligned >1 times 99.01% overall alignment rate Time searching: 00:31:30 Overall time: 00:31:30 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 36 files... [bam_rmdupse_core] 68864892 / 86512446 = 0.7960 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 20:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.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 20:26:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:26:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:26:17: 1000000 INFO @ Thu, 08 Oct 2020 20:26:24: 2000000 INFO @ Thu, 08 Oct 2020 20:26:32: 3000000 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 20:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.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 20:26:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:26:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:26:39: 4000000 INFO @ Thu, 08 Oct 2020 20:26:45: 1000000 INFO @ Thu, 08 Oct 2020 20:26:47: 5000000 INFO @ Thu, 08 Oct 2020 20:26:51: 2000000 INFO @ Thu, 08 Oct 2020 20:26:56: 6000000 INFO @ Thu, 08 Oct 2020 20:26:57: 3000000 INFO @ Thu, 08 Oct 2020 20:27:03: 4000000 INFO @ Thu, 08 Oct 2020 20:27:04: 7000000 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 20:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.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 20:27:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:27:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:27:09: 5000000 INFO @ Thu, 08 Oct 2020 20:27:13: 8000000 INFO @ Thu, 08 Oct 2020 20:27:15: 1000000 INFO @ Thu, 08 Oct 2020 20:27:16: 6000000 INFO @ Thu, 08 Oct 2020 20:27:21: 2000000 INFO @ Thu, 08 Oct 2020 20:27:21: 9000000 INFO @ Thu, 08 Oct 2020 20:27:23: 7000000 INFO @ Thu, 08 Oct 2020 20:27:27: 3000000 INFO @ Thu, 08 Oct 2020 20:27:29: 8000000 INFO @ Thu, 08 Oct 2020 20:27:30: 10000000 INFO @ Thu, 08 Oct 2020 20:27:33: 4000000 INFO @ Thu, 08 Oct 2020 20:27:35: 9000000 INFO @ Thu, 08 Oct 2020 20:27:38: 11000000 INFO @ Thu, 08 Oct 2020 20:27:39: 5000000 INFO @ Thu, 08 Oct 2020 20:27:42: 10000000 INFO @ Thu, 08 Oct 2020 20:27:45: 6000000 INFO @ Thu, 08 Oct 2020 20:27:46: 12000000 INFO @ Thu, 08 Oct 2020 20:27:48: 11000000 INFO @ Thu, 08 Oct 2020 20:27:52: 7000000 INFO @ Thu, 08 Oct 2020 20:27:54: 13000000 INFO @ Thu, 08 Oct 2020 20:27:54: 12000000 INFO @ Thu, 08 Oct 2020 20:27:58: 8000000 INFO @ Thu, 08 Oct 2020 20:28:01: 13000000 INFO @ Thu, 08 Oct 2020 20:28:02: 14000000 INFO @ Thu, 08 Oct 2020 20:28:04: 9000000 INFO @ Thu, 08 Oct 2020 20:28:07: 14000000 INFO @ Thu, 08 Oct 2020 20:28:10: 15000000 INFO @ Thu, 08 Oct 2020 20:28:10: 10000000 INFO @ Thu, 08 Oct 2020 20:28:13: 15000000 INFO @ Thu, 08 Oct 2020 20:28:16: 11000000 INFO @ Thu, 08 Oct 2020 20:28:18: 16000000 INFO @ Thu, 08 Oct 2020 20:28:19: 16000000 INFO @ Thu, 08 Oct 2020 20:28:22: 12000000 INFO @ Thu, 08 Oct 2020 20:28:26: 17000000 INFO @ Thu, 08 Oct 2020 20:28:26: 17000000 INFO @ Thu, 08 Oct 2020 20:28:29: 13000000 INFO @ Thu, 08 Oct 2020 20:28:31: #1 tag size is determined as 72 bps INFO @ Thu, 08 Oct 2020 20:28:31: #1 tag size = 72 INFO @ Thu, 08 Oct 2020 20:28:31: #1 total tags in treatment: 17647554 INFO @ Thu, 08 Oct 2020 20:28:31: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:31: #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 20:28:31: #1 tags after filtering in treatment: 17647554 INFO @ Thu, 08 Oct 2020 20:28:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:31: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:31: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:31: #1 tag size is determined as 72 bps INFO @ Thu, 08 Oct 2020 20:28:31: #1 tag size = 72 INFO @ Thu, 08 Oct 2020 20:28:31: #1 total tags in treatment: 17647554 INFO @ Thu, 08 Oct 2020 20:28:31: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:31: #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 20:28:32: #1 tags after filtering in treatment: 17647554 INFO @ Thu, 08 Oct 2020 20:28:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:32: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:32: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:32: #2 number of paired peaks: 492 WARNING @ Thu, 08 Oct 2020 20:28:32: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Thu, 08 Oct 2020 20:28:32: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:32: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:32: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:32: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:32: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:28:32: #2 alternative fragment length(s) may be 1,25,41,571 bps INFO @ Thu, 08 Oct 2020 20:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.10_model.r WARNING @ Thu, 08 Oct 2020 20:28:32: #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 20:28:32: #2 You may need to consider one of the other alternative d(s): 1,25,41,571 WARNING @ Thu, 08 Oct 2020 20:28:32: #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 20:28:32: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:28:33: #2 number of paired peaks: 492 WARNING @ Thu, 08 Oct 2020 20:28:33: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Thu, 08 Oct 2020 20:28:33: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:33: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:33: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:33: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:33: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:28:33: #2 alternative fragment length(s) may be 1,25,41,571 bps INFO @ Thu, 08 Oct 2020 20:28:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.05_model.r WARNING @ Thu, 08 Oct 2020 20:28:33: #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 20:28:33: #2 You may need to consider one of the other alternative d(s): 1,25,41,571 WARNING @ Thu, 08 Oct 2020 20:28:33: #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 20:28:33: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:28:34: 14000000 INFO @ Thu, 08 Oct 2020 20:28:40: 15000000 INFO @ Thu, 08 Oct 2020 20:28:46: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:28:52: 17000000 INFO @ Thu, 08 Oct 2020 20:28:56: #1 tag size is determined as 72 bps INFO @ Thu, 08 Oct 2020 20:28:56: #1 tag size = 72 INFO @ Thu, 08 Oct 2020 20:28:56: #1 total tags in treatment: 17647554 INFO @ Thu, 08 Oct 2020 20:28:56: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:56: #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 20:28:56: #1 tags after filtering in treatment: 17647554 INFO @ Thu, 08 Oct 2020 20:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:56: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:56: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:58: #2 number of paired peaks: 492 WARNING @ Thu, 08 Oct 2020 20:28:58: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Thu, 08 Oct 2020 20:28:58: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:58: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:58: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:58: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:58: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:28:58: #2 alternative fragment length(s) may be 1,25,41,571 bps INFO @ Thu, 08 Oct 2020 20:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.20_model.r WARNING @ Thu, 08 Oct 2020 20:28:58: #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 20:28:58: #2 You may need to consider one of the other alternative d(s): 1,25,41,571 WARNING @ Thu, 08 Oct 2020 20:28:58: #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 20:28:58: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:29:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:29:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.10_summits.bed INFO @ Thu, 08 Oct 2020 20:29:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.05_summits.bed INFO @ Thu, 08 Oct 2020 20:29:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:29:26: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331152/SRX8331152.20_summits.bed INFO @ Thu, 08 Oct 2020 20:29:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling