Job ID = 6366559 SRX = SRX1936237 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:37 prefetch.2.10.7: 1) Downloading 'SRR3879844'... 2020-06-15T22:47:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:32 prefetch.2.10.7: 1) 'SRR3879844' was downloaded successfully Read 22293459 spots for SRR3879844/SRR3879844.sra Written 22293459 spots for SRR3879844/SRR3879844.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:08 22293459 reads; of these: 22293459 (100.00%) were unpaired; of these: 1266031 (5.68%) aligned 0 times 17529006 (78.63%) aligned exactly 1 time 3498422 (15.69%) aligned >1 times 94.32% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 2682430 / 21027428 = 0.1276 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 @ Tue, 16 Jun 2020 08:01:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.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 @ Tue, 16 Jun 2020 08:01:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:14: 1000000 INFO @ Tue, 16 Jun 2020 08:01:20: 2000000 INFO @ Tue, 16 Jun 2020 08:01:25: 3000000 INFO @ Tue, 16 Jun 2020 08:01:31: 4000000 INFO @ Tue, 16 Jun 2020 08:01:36: 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 @ Tue, 16 Jun 2020 08:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.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 @ Tue, 16 Jun 2020 08:01:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:42: 6000000 INFO @ Tue, 16 Jun 2020 08:01:45: 1000000 INFO @ Tue, 16 Jun 2020 08:01:49: 7000000 INFO @ Tue, 16 Jun 2020 08:01:51: 2000000 INFO @ Tue, 16 Jun 2020 08:01:55: 8000000 INFO @ Tue, 16 Jun 2020 08:01:57: 3000000 INFO @ Tue, 16 Jun 2020 08:02:02: 9000000 INFO @ Tue, 16 Jun 2020 08:02:03: 4000000 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 @ Tue, 16 Jun 2020 08:02:08: 10000000 INFO @ Tue, 16 Jun 2020 08:02:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.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 @ Tue, 16 Jun 2020 08:02:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:10: 5000000 INFO @ Tue, 16 Jun 2020 08:02:15: 11000000 INFO @ Tue, 16 Jun 2020 08:02:16: 1000000 INFO @ Tue, 16 Jun 2020 08:02:17: 6000000 INFO @ Tue, 16 Jun 2020 08:02:22: 12000000 INFO @ Tue, 16 Jun 2020 08:02:23: 7000000 INFO @ Tue, 16 Jun 2020 08:02:24: 2000000 INFO @ Tue, 16 Jun 2020 08:02:29: 13000000 INFO @ Tue, 16 Jun 2020 08:02:30: 8000000 INFO @ Tue, 16 Jun 2020 08:02:31: 3000000 INFO @ Tue, 16 Jun 2020 08:02:36: 14000000 INFO @ Tue, 16 Jun 2020 08:02:37: 9000000 INFO @ Tue, 16 Jun 2020 08:02:39: 4000000 INFO @ Tue, 16 Jun 2020 08:02:42: 15000000 INFO @ Tue, 16 Jun 2020 08:02:44: 10000000 INFO @ Tue, 16 Jun 2020 08:02:46: 5000000 INFO @ Tue, 16 Jun 2020 08:02:49: 16000000 INFO @ Tue, 16 Jun 2020 08:02:50: 11000000 INFO @ Tue, 16 Jun 2020 08:02:54: 6000000 INFO @ Tue, 16 Jun 2020 08:02:56: 17000000 INFO @ Tue, 16 Jun 2020 08:02:57: 12000000 INFO @ Tue, 16 Jun 2020 08:03:02: 7000000 INFO @ Tue, 16 Jun 2020 08:03:02: 18000000 INFO @ Tue, 16 Jun 2020 08:03:04: 13000000 INFO @ Tue, 16 Jun 2020 08:03:05: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:03:05: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:03:05: #1 total tags in treatment: 18344998 INFO @ Tue, 16 Jun 2020 08:03:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:03:05: #1 tags after filtering in treatment: 18344998 INFO @ Tue, 16 Jun 2020 08:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:06: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:03:06: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:06: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:03:06: #2 alternative fragment length(s) may be 2,46,549,596 bps INFO @ Tue, 16 Jun 2020 08:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:06: #2 You may need to consider one of the other alternative d(s): 2,46,549,596 WARNING @ Tue, 16 Jun 2020 08:03:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:03:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:09: 8000000 INFO @ Tue, 16 Jun 2020 08:03:10: 14000000 INFO @ Tue, 16 Jun 2020 08:03:16: 15000000 INFO @ Tue, 16 Jun 2020 08:03:17: 9000000 INFO @ Tue, 16 Jun 2020 08:03:23: 16000000 INFO @ Tue, 16 Jun 2020 08:03:24: 10000000 INFO @ Tue, 16 Jun 2020 08:03:29: 17000000 INFO @ Tue, 16 Jun 2020 08:03:31: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:36: 18000000 INFO @ Tue, 16 Jun 2020 08:03:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:38: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:03:38: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:03:38: #1 total tags in treatment: 18344998 INFO @ Tue, 16 Jun 2020 08:03:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:03:38: #1 tags after filtering in treatment: 18344998 INFO @ Tue, 16 Jun 2020 08:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:39: 12000000 INFO @ Tue, 16 Jun 2020 08:03:40: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:03:40: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:40: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:03:40: #2 alternative fragment length(s) may be 2,46,549,596 bps INFO @ Tue, 16 Jun 2020 08:03:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.10_model.r WARNING @ Tue, 16 Jun 2020 08:03:40: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:40: #2 You may need to consider one of the other alternative d(s): 2,46,549,596 WARNING @ Tue, 16 Jun 2020 08:03:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:03:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:46: 13000000 INFO @ Tue, 16 Jun 2020 08:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:53: 14000000 INFO @ Tue, 16 Jun 2020 08:03:59: 15000000 INFO @ Tue, 16 Jun 2020 08:04:06: 16000000 INFO @ Tue, 16 Jun 2020 08:04:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:13: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:20: 18000000 INFO @ Tue, 16 Jun 2020 08:04:23: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:04:23: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:04:23: #1 total tags in treatment: 18344998 INFO @ Tue, 16 Jun 2020 08:04:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:04:23: #1 tags after filtering in treatment: 18344998 INFO @ Tue, 16 Jun 2020 08:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:24: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:04:24: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:24: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:04:24: #2 alternative fragment length(s) may be 2,46,549,596 bps INFO @ Tue, 16 Jun 2020 08:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:24: #2 You may need to consider one of the other alternative d(s): 2,46,549,596 WARNING @ Tue, 16 Jun 2020 08:04:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:04:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936237/SRX1936237.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling