Job ID = 6367578 SRX = SRX331334 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:01 prefetch.2.10.7: 1) Downloading 'SRR947571'... 2020-06-15T23:25:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:44 prefetch.2.10.7: 1) 'SRR947571' was downloaded successfully Read 21509609 spots for SRR947571/SRR947571.sra Written 21509609 spots for SRR947571/SRR947571.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: 00:03:51 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255420 (1.19%) aligned 0 times 17821585 (82.85%) aligned exactly 1 time 3432604 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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 8 files... [bam_rmdupse_core] 3667441 / 21254189 = 0.1726 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 08:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.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 08:39:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:33: 1000000 INFO @ Tue, 16 Jun 2020 08:39:39: 2000000 INFO @ Tue, 16 Jun 2020 08:39:44: 3000000 INFO @ Tue, 16 Jun 2020 08:39:50: 4000000 INFO @ Tue, 16 Jun 2020 08:39:55: 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 08:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.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 08:39:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:01: 6000000 INFO @ Tue, 16 Jun 2020 08:40:05: 1000000 INFO @ Tue, 16 Jun 2020 08:40:08: 7000000 INFO @ Tue, 16 Jun 2020 08:40:12: 2000000 INFO @ Tue, 16 Jun 2020 08:40:15: 8000000 INFO @ Tue, 16 Jun 2020 08:40:19: 3000000 INFO @ Tue, 16 Jun 2020 08:40:22: 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 08:40:27: 4000000 INFO @ Tue, 16 Jun 2020 08:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.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 08:40:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:28: 10000000 INFO @ Tue, 16 Jun 2020 08:40:34: 5000000 INFO @ Tue, 16 Jun 2020 08:40:35: 1000000 INFO @ Tue, 16 Jun 2020 08:40:35: 11000000 INFO @ Tue, 16 Jun 2020 08:40:42: 2000000 INFO @ Tue, 16 Jun 2020 08:40:42: 6000000 INFO @ Tue, 16 Jun 2020 08:40:42: 12000000 INFO @ Tue, 16 Jun 2020 08:40:49: 3000000 INFO @ Tue, 16 Jun 2020 08:40:49: 13000000 INFO @ Tue, 16 Jun 2020 08:40:49: 7000000 INFO @ Tue, 16 Jun 2020 08:40:55: 4000000 INFO @ Tue, 16 Jun 2020 08:40:56: 14000000 INFO @ Tue, 16 Jun 2020 08:40:57: 8000000 INFO @ Tue, 16 Jun 2020 08:41:02: 5000000 INFO @ Tue, 16 Jun 2020 08:41:03: 15000000 INFO @ Tue, 16 Jun 2020 08:41:05: 9000000 INFO @ Tue, 16 Jun 2020 08:41:09: 6000000 INFO @ Tue, 16 Jun 2020 08:41:10: 16000000 INFO @ Tue, 16 Jun 2020 08:41:13: 10000000 INFO @ Tue, 16 Jun 2020 08:41:16: 7000000 INFO @ Tue, 16 Jun 2020 08:41:17: 17000000 INFO @ Tue, 16 Jun 2020 08:41:21: 11000000 INFO @ Tue, 16 Jun 2020 08:41:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:41:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:41:21: #1 total tags in treatment: 17586748 INFO @ Tue, 16 Jun 2020 08:41:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:21: #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 08:41:22: #1 tags after filtering in treatment: 17586748 INFO @ Tue, 16 Jun 2020 08:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:23: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:41:23: 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 08:41:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:23: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:41:23: #2 alternative fragment length(s) may be 1,35,562,585 bps INFO @ Tue, 16 Jun 2020 08:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:23: #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 08:41:23: #2 You may need to consider one of the other alternative d(s): 1,35,562,585 WARNING @ Tue, 16 Jun 2020 08:41:23: #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 08:41:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:23: 8000000 INFO @ Tue, 16 Jun 2020 08:41:29: 12000000 INFO @ Tue, 16 Jun 2020 08:41:30: 9000000 INFO @ Tue, 16 Jun 2020 08:41:36: 13000000 INFO @ Tue, 16 Jun 2020 08:41:37: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:44: 11000000 INFO @ Tue, 16 Jun 2020 08:41:45: 14000000 INFO @ Tue, 16 Jun 2020 08:41:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:51: 12000000 INFO @ Tue, 16 Jun 2020 08:41:53: 15000000 INFO @ Tue, 16 Jun 2020 08:41:59: 13000000 INFO @ Tue, 16 Jun 2020 08:42:01: 16000000 INFO @ Tue, 16 Jun 2020 08:42:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:03: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:06: 14000000 INFO @ Tue, 16 Jun 2020 08:42:09: 17000000 INFO @ Tue, 16 Jun 2020 08:42:13: 15000000 INFO @ Tue, 16 Jun 2020 08:42:13: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:42:13: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:42:13: #1 total tags in treatment: 17586748 INFO @ Tue, 16 Jun 2020 08:42:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:13: #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 08:42:14: #1 tags after filtering in treatment: 17586748 INFO @ Tue, 16 Jun 2020 08:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:15: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:42:15: 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 08:42:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:15: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:42:15: #2 alternative fragment length(s) may be 1,35,562,585 bps INFO @ Tue, 16 Jun 2020 08:42:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.10_model.r WARNING @ Tue, 16 Jun 2020 08:42:15: #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 08:42:15: #2 You may need to consider one of the other alternative d(s): 1,35,562,585 WARNING @ Tue, 16 Jun 2020 08:42:15: #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 08:42:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:19: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:42:25: 17000000 INFO @ Tue, 16 Jun 2020 08:42:29: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:42:29: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:42:29: #1 total tags in treatment: 17586748 INFO @ Tue, 16 Jun 2020 08:42:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:29: #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 08:42:29: #1 tags after filtering in treatment: 17586748 INFO @ Tue, 16 Jun 2020 08:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:31: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:42:31: 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 08:42:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:42:31: #2 alternative fragment length(s) may be 1,35,562,585 bps INFO @ Tue, 16 Jun 2020 08:42:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:31: #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 08:42:31: #2 You may need to consider one of the other alternative d(s): 1,35,562,585 WARNING @ Tue, 16 Jun 2020 08:42:31: #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 08:42:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331334/SRX331334.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling