Job ID = 10165770 SRX = SRX9120606 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37410483 spots for SRR12638549/SRR12638549.sra Written 37410483 spots for SRR12638549/SRR12638549.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166080 ("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: 00:07:33 37410483 reads; of these: 37410483 (100.00%) were unpaired; of these: 6039515 (16.14%) aligned 0 times 26041190 (69.61%) aligned exactly 1 time 5329778 (14.25%) aligned >1 times 83.86% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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 16 files... [bam_rmdupse_core] 6015806 / 31370968 = 0.1918 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/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.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 20:03:43: 1000000 INFO @ Thu, 08 Oct 2020 20:03:48: 2000000 INFO @ Thu, 08 Oct 2020 20:03:53: 3000000 INFO @ Thu, 08 Oct 2020 20:03:58: 4000000 INFO @ Thu, 08 Oct 2020 20:04:03: 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 20:04:07: 6000000 INFO @ Thu, 08 Oct 2020 20:04:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.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 20:04:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:12: 7000000 INFO @ Thu, 08 Oct 2020 20:04:14: 1000000 INFO @ Thu, 08 Oct 2020 20:04:17: 8000000 INFO @ Thu, 08 Oct 2020 20:04:19: 2000000 INFO @ Thu, 08 Oct 2020 20:04:22: 9000000 INFO @ Thu, 08 Oct 2020 20:04:24: 3000000 INFO @ Thu, 08 Oct 2020 20:04:27: 10000000 INFO @ Thu, 08 Oct 2020 20:04:29: 4000000 INFO @ Thu, 08 Oct 2020 20:04:32: 11000000 INFO @ Thu, 08 Oct 2020 20:04:34: 5000000 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: 12000000 INFO @ Thu, 08 Oct 2020 20:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.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 20:04:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:39: 6000000 INFO @ Thu, 08 Oct 2020 20:04:43: 13000000 INFO @ Thu, 08 Oct 2020 20:04:44: 1000000 INFO @ Thu, 08 Oct 2020 20:04:44: 7000000 INFO @ Thu, 08 Oct 2020 20:04:48: 14000000 INFO @ Thu, 08 Oct 2020 20:04:49: 2000000 INFO @ Thu, 08 Oct 2020 20:04:49: 8000000 INFO @ Thu, 08 Oct 2020 20:04:53: 15000000 INFO @ Thu, 08 Oct 2020 20:04:54: 3000000 INFO @ Thu, 08 Oct 2020 20:04:54: 9000000 INFO @ Thu, 08 Oct 2020 20:04:59: 16000000 INFO @ Thu, 08 Oct 2020 20:04:59: 4000000 INFO @ Thu, 08 Oct 2020 20:05:00: 10000000 INFO @ Thu, 08 Oct 2020 20:05:04: 17000000 INFO @ Thu, 08 Oct 2020 20:05:05: 5000000 INFO @ Thu, 08 Oct 2020 20:05:05: 11000000 INFO @ Thu, 08 Oct 2020 20:05:09: 18000000 INFO @ Thu, 08 Oct 2020 20:05:10: 6000000 INFO @ Thu, 08 Oct 2020 20:05:10: 12000000 INFO @ Thu, 08 Oct 2020 20:05:14: 19000000 INFO @ Thu, 08 Oct 2020 20:05:15: 7000000 INFO @ Thu, 08 Oct 2020 20:05:15: 13000000 INFO @ Thu, 08 Oct 2020 20:05:19: 20000000 INFO @ Thu, 08 Oct 2020 20:05:20: 8000000 INFO @ Thu, 08 Oct 2020 20:05:21: 14000000 INFO @ Thu, 08 Oct 2020 20:05:25: 21000000 INFO @ Thu, 08 Oct 2020 20:05:26: 9000000 INFO @ Thu, 08 Oct 2020 20:05:26: 15000000 INFO @ Thu, 08 Oct 2020 20:05:30: 22000000 INFO @ Thu, 08 Oct 2020 20:05:31: 10000000 INFO @ Thu, 08 Oct 2020 20:05:31: 16000000 INFO @ Thu, 08 Oct 2020 20:05:35: 23000000 INFO @ Thu, 08 Oct 2020 20:05:36: 11000000 INFO @ Thu, 08 Oct 2020 20:05:36: 17000000 INFO @ Thu, 08 Oct 2020 20:05:40: 24000000 INFO @ Thu, 08 Oct 2020 20:05:41: 12000000 INFO @ Thu, 08 Oct 2020 20:05:41: 18000000 INFO @ Thu, 08 Oct 2020 20:05:45: 25000000 INFO @ Thu, 08 Oct 2020 20:05:47: 19000000 INFO @ Thu, 08 Oct 2020 20:05:47: 13000000 INFO @ Thu, 08 Oct 2020 20:05:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:05:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:05:47: #1 total tags in treatment: 25355162 INFO @ Thu, 08 Oct 2020 20:05:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:05:47: #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 20:05:48: #1 tags after filtering in treatment: 25355162 INFO @ Thu, 08 Oct 2020 20:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:05:48: #1 finished! INFO @ Thu, 08 Oct 2020 20:05:48: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:05:49: #2 number of paired peaks: 158 WARNING @ Thu, 08 Oct 2020 20:05:49: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Thu, 08 Oct 2020 20:05:49: start model_add_line... INFO @ Thu, 08 Oct 2020 20:05:49: start X-correlation... INFO @ Thu, 08 Oct 2020 20:05:49: end of X-cor INFO @ Thu, 08 Oct 2020 20:05:49: #2 finished! INFO @ Thu, 08 Oct 2020 20:05:49: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:05:49: #2 alternative fragment length(s) may be 1,26,41,585 bps INFO @ Thu, 08 Oct 2020 20:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.05_model.r WARNING @ Thu, 08 Oct 2020 20:05:49: #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 20:05:49: #2 You may need to consider one of the other alternative d(s): 1,26,41,585 WARNING @ Thu, 08 Oct 2020 20:05:49: #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 20:05:49: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:05:52: 20000000 INFO @ Thu, 08 Oct 2020 20:05:52: 14000000 INFO @ Thu, 08 Oct 2020 20:05:57: 21000000 INFO @ Thu, 08 Oct 2020 20:05:57: 15000000 INFO @ Thu, 08 Oct 2020 20:06:02: 22000000 INFO @ Thu, 08 Oct 2020 20:06:02: 16000000 INFO @ Thu, 08 Oct 2020 20:06:07: 23000000 INFO @ Thu, 08 Oct 2020 20:06:07: 17000000 INFO @ Thu, 08 Oct 2020 20:06:12: 24000000 INFO @ Thu, 08 Oct 2020 20:06:12: 18000000 INFO @ Thu, 08 Oct 2020 20:06:17: 25000000 INFO @ Thu, 08 Oct 2020 20:06:17: 19000000 INFO @ Thu, 08 Oct 2020 20:06:19: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:19: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:19: #1 total tags in treatment: 25355162 INFO @ Thu, 08 Oct 2020 20:06:19: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:19: #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 20:06:19: #1 tags after filtering in treatment: 25355162 INFO @ Thu, 08 Oct 2020 20:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:19: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:19: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:21: #2 number of paired peaks: 158 WARNING @ Thu, 08 Oct 2020 20:06:21: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:21: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:21: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:21: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:21: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:21: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:21: #2 alternative fragment length(s) may be 1,26,41,585 bps INFO @ Thu, 08 Oct 2020 20:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.10_model.r WARNING @ Thu, 08 Oct 2020 20:06:21: #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 20:06:21: #2 You may need to consider one of the other alternative d(s): 1,26,41,585 WARNING @ Thu, 08 Oct 2020 20:06:21: #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 20:06:21: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:22: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:06:27: 21000000 INFO @ Thu, 08 Oct 2020 20:06:27: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:32: 22000000 INFO @ Thu, 08 Oct 2020 20:06:37: 23000000 INFO @ Thu, 08 Oct 2020 20:06:42: 24000000 INFO @ Thu, 08 Oct 2020 20:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.05_summits.bed INFO @ Thu, 08 Oct 2020 20:06:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:06:47: 25000000 INFO @ Thu, 08 Oct 2020 20:06:49: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:49: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:49: #1 total tags in treatment: 25355162 INFO @ Thu, 08 Oct 2020 20:06:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:49: #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 20:06:49: #1 tags after filtering in treatment: 25355162 INFO @ Thu, 08 Oct 2020 20:06:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:49: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:51: #2 number of paired peaks: 158 WARNING @ Thu, 08 Oct 2020 20:06:51: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:51: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:51: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:51: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:51: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:51: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:51: #2 alternative fragment length(s) may be 1,26,41,585 bps INFO @ Thu, 08 Oct 2020 20:06:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.20_model.r WARNING @ Thu, 08 Oct 2020 20:06:51: #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 20:06:51: #2 You may need to consider one of the other alternative d(s): 1,26,41,585 WARNING @ Thu, 08 Oct 2020 20:06:51: #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 20:06:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.10_summits.bed INFO @ Thu, 08 Oct 2020 20:07:17: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120606/SRX9120606.20_summits.bed INFO @ Thu, 08 Oct 2020 20:07:46: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling