Job ID = 6366655 SRX = SRX216754 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:46 prefetch.2.10.7: 1) Downloading 'SRR648389'... 2020-06-15T23:20:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:52 prefetch.2.10.7: 1) 'SRR648389' was downloaded successfully Read 23260651 spots for SRR648389/SRR648389.sra Written 23260651 spots for SRR648389/SRR648389.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: 00:05:17 23260651 reads; of these: 23260651 (100.00%) were unpaired; of these: 1390099 (5.98%) aligned 0 times 18612961 (80.02%) aligned exactly 1 time 3257591 (14.00%) aligned >1 times 94.02% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 2367906 / 21870552 = 0.1083 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 08:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.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 08:34:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:00: 1000000 INFO @ Tue, 16 Jun 2020 08:35:06: 2000000 INFO @ Tue, 16 Jun 2020 08:35:12: 3000000 INFO @ Tue, 16 Jun 2020 08:35:18: 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 @ Tue, 16 Jun 2020 08:35:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.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 08:35:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:25: 5000000 INFO @ Tue, 16 Jun 2020 08:35:30: 1000000 INFO @ Tue, 16 Jun 2020 08:35:31: 6000000 INFO @ Tue, 16 Jun 2020 08:35:36: 2000000 INFO @ Tue, 16 Jun 2020 08:35:38: 7000000 INFO @ Tue, 16 Jun 2020 08:35:42: 3000000 INFO @ Tue, 16 Jun 2020 08:35:44: 8000000 INFO @ Tue, 16 Jun 2020 08:35:48: 4000000 INFO @ Tue, 16 Jun 2020 08:35:50: 9000000 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 08:35:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.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 08:35:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:54: 5000000 INFO @ Tue, 16 Jun 2020 08:35:56: 10000000 INFO @ Tue, 16 Jun 2020 08:35:59: 1000000 INFO @ Tue, 16 Jun 2020 08:36:00: 6000000 INFO @ Tue, 16 Jun 2020 08:36:03: 11000000 INFO @ Tue, 16 Jun 2020 08:36:05: 2000000 INFO @ Tue, 16 Jun 2020 08:36:06: 7000000 INFO @ Tue, 16 Jun 2020 08:36:09: 12000000 INFO @ Tue, 16 Jun 2020 08:36:11: 3000000 INFO @ Tue, 16 Jun 2020 08:36:13: 8000000 INFO @ Tue, 16 Jun 2020 08:36:15: 13000000 INFO @ Tue, 16 Jun 2020 08:36:16: 4000000 INFO @ Tue, 16 Jun 2020 08:36:19: 9000000 INFO @ Tue, 16 Jun 2020 08:36:21: 14000000 INFO @ Tue, 16 Jun 2020 08:36:22: 5000000 INFO @ Tue, 16 Jun 2020 08:36:25: 10000000 INFO @ Tue, 16 Jun 2020 08:36:27: 6000000 INFO @ Tue, 16 Jun 2020 08:36:27: 15000000 INFO @ Tue, 16 Jun 2020 08:36:31: 11000000 INFO @ Tue, 16 Jun 2020 08:36:33: 7000000 INFO @ Tue, 16 Jun 2020 08:36:34: 16000000 INFO @ Tue, 16 Jun 2020 08:36:37: 12000000 INFO @ Tue, 16 Jun 2020 08:36:38: 8000000 INFO @ Tue, 16 Jun 2020 08:36:40: 17000000 INFO @ Tue, 16 Jun 2020 08:36:43: 13000000 INFO @ Tue, 16 Jun 2020 08:36:44: 9000000 INFO @ Tue, 16 Jun 2020 08:36:46: 18000000 INFO @ Tue, 16 Jun 2020 08:36:49: 10000000 INFO @ Tue, 16 Jun 2020 08:36:49: 14000000 INFO @ Tue, 16 Jun 2020 08:36:52: 19000000 INFO @ Tue, 16 Jun 2020 08:36:55: 11000000 INFO @ Tue, 16 Jun 2020 08:36:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:36:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:36:55: #1 total tags in treatment: 19502646 INFO @ Tue, 16 Jun 2020 08:36:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:55: #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 08:36:56: 15000000 INFO @ Tue, 16 Jun 2020 08:36:56: #1 tags after filtering in treatment: 19502646 INFO @ Tue, 16 Jun 2020 08:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:57: #2 number of paired peaks: 203 WARNING @ Tue, 16 Jun 2020 08:36:57: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:57: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:36:57: #2 alternative fragment length(s) may be 1,48,571 bps INFO @ Tue, 16 Jun 2020 08:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:57: #2 You may need to consider one of the other alternative d(s): 1,48,571 WARNING @ Tue, 16 Jun 2020 08:36:57: #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 08:36:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:00: 12000000 INFO @ Tue, 16 Jun 2020 08:37:02: 16000000 INFO @ Tue, 16 Jun 2020 08:37:06: 13000000 INFO @ Tue, 16 Jun 2020 08:37:08: 17000000 INFO @ Tue, 16 Jun 2020 08:37:11: 14000000 INFO @ Tue, 16 Jun 2020 08:37:14: 18000000 INFO @ Tue, 16 Jun 2020 08:37:17: 15000000 INFO @ Tue, 16 Jun 2020 08:37:20: 19000000 INFO @ Tue, 16 Jun 2020 08:37:22: 16000000 INFO @ Tue, 16 Jun 2020 08:37:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:37:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:37:24: #1 total tags in treatment: 19502646 INFO @ Tue, 16 Jun 2020 08:37:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:24: #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 08:37:24: #1 tags after filtering in treatment: 19502646 INFO @ Tue, 16 Jun 2020 08:37:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:25: #2 number of paired peaks: 203 WARNING @ Tue, 16 Jun 2020 08:37:25: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:37:25: #2 alternative fragment length(s) may be 1,48,571 bps INFO @ Tue, 16 Jun 2020 08:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.10_model.r WARNING @ Tue, 16 Jun 2020 08:37:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:25: #2 You may need to consider one of the other alternative d(s): 1,48,571 WARNING @ Tue, 16 Jun 2020 08:37:25: #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 08:37:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:27: 17000000 INFO @ Tue, 16 Jun 2020 08:37:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:33: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:38: 19000000 INFO @ Tue, 16 Jun 2020 08:37:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:37:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:37:41: #1 total tags in treatment: 19502646 INFO @ Tue, 16 Jun 2020 08:37:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:41: #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 08:37:41: #1 tags after filtering in treatment: 19502646 INFO @ Tue, 16 Jun 2020 08:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:42: #2 number of paired peaks: 203 WARNING @ Tue, 16 Jun 2020 08:37:42: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:42: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:37:42: #2 alternative fragment length(s) may be 1,48,571 bps INFO @ Tue, 16 Jun 2020 08:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:42: #2 You may need to consider one of the other alternative d(s): 1,48,571 WARNING @ Tue, 16 Jun 2020 08:37:42: #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 08:37:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.10_summits.bed INFO @ Tue, 16 Jun 2020 08:38:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216754/SRX216754.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling