Job ID = 6368647 SRX = SRX529207 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:21 prefetch.2.10.7: 1) Downloading 'SRR1265811'... 2020-06-16T00:21:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:58 prefetch.2.10.7: 1) 'SRR1265811' was downloaded successfully Read 19874451 spots for SRR1265811/SRR1265811.sra Written 19874451 spots for SRR1265811/SRR1265811.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: 00:03:28 19874451 reads; of these: 19874451 (100.00%) were unpaired; of these: 311473 (1.57%) aligned 0 times 16205481 (81.54%) aligned exactly 1 time 3357497 (16.89%) aligned >1 times 98.43% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 2055522 / 19562978 = 0.1051 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 09:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.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 09:35:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:10: 1000000 INFO @ Tue, 16 Jun 2020 09:35:16: 2000000 INFO @ Tue, 16 Jun 2020 09:35:23: 3000000 INFO @ Tue, 16 Jun 2020 09:35:30: 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 09:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.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 09:35:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:36: 5000000 INFO @ Tue, 16 Jun 2020 09:35:40: 1000000 INFO @ Tue, 16 Jun 2020 09:35:42: 6000000 INFO @ Tue, 16 Jun 2020 09:35:46: 2000000 INFO @ Tue, 16 Jun 2020 09:35:49: 7000000 INFO @ Tue, 16 Jun 2020 09:35:52: 3000000 INFO @ Tue, 16 Jun 2020 09:35:55: 8000000 INFO @ Tue, 16 Jun 2020 09:35:58: 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 09:36:01: 9000000 INFO @ Tue, 16 Jun 2020 09:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.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 09:36:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:04: 5000000 INFO @ Tue, 16 Jun 2020 09:36:08: 10000000 INFO @ Tue, 16 Jun 2020 09:36:10: 1000000 INFO @ Tue, 16 Jun 2020 09:36:11: 6000000 INFO @ Tue, 16 Jun 2020 09:36:14: 11000000 INFO @ Tue, 16 Jun 2020 09:36:17: 7000000 INFO @ Tue, 16 Jun 2020 09:36:17: 2000000 INFO @ Tue, 16 Jun 2020 09:36:21: 12000000 INFO @ Tue, 16 Jun 2020 09:36:23: 8000000 INFO @ Tue, 16 Jun 2020 09:36:24: 3000000 INFO @ Tue, 16 Jun 2020 09:36:28: 13000000 INFO @ Tue, 16 Jun 2020 09:36:29: 9000000 INFO @ Tue, 16 Jun 2020 09:36:30: 4000000 INFO @ Tue, 16 Jun 2020 09:36:34: 14000000 INFO @ Tue, 16 Jun 2020 09:36:36: 10000000 INFO @ Tue, 16 Jun 2020 09:36:37: 5000000 INFO @ Tue, 16 Jun 2020 09:36:41: 15000000 INFO @ Tue, 16 Jun 2020 09:36:42: 11000000 INFO @ Tue, 16 Jun 2020 09:36:44: 6000000 INFO @ Tue, 16 Jun 2020 09:36:48: 16000000 INFO @ Tue, 16 Jun 2020 09:36:48: 12000000 INFO @ Tue, 16 Jun 2020 09:36:50: 7000000 INFO @ Tue, 16 Jun 2020 09:36:54: 13000000 INFO @ Tue, 16 Jun 2020 09:36:54: 17000000 INFO @ Tue, 16 Jun 2020 09:36:57: 8000000 INFO @ Tue, 16 Jun 2020 09:36:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:36:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:36:58: #1 total tags in treatment: 17507456 INFO @ Tue, 16 Jun 2020 09:36:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:58: #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 09:36:58: #1 tags after filtering in treatment: 17507456 INFO @ Tue, 16 Jun 2020 09:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:59: #2 number of paired peaks: 168 WARNING @ Tue, 16 Jun 2020 09:36:59: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:59: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:36:59: #2 alternative fragment length(s) may be 2,23,37,521,534,597 bps INFO @ Tue, 16 Jun 2020 09:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:59: #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 09:36:59: #2 You may need to consider one of the other alternative d(s): 2,23,37,521,534,597 WARNING @ Tue, 16 Jun 2020 09:36:59: #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 09:36:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:00: 14000000 INFO @ Tue, 16 Jun 2020 09:37:03: 9000000 INFO @ Tue, 16 Jun 2020 09:37:07: 15000000 INFO @ Tue, 16 Jun 2020 09:37:09: 10000000 INFO @ Tue, 16 Jun 2020 09:37:13: 16000000 INFO @ Tue, 16 Jun 2020 09:37:16: 11000000 INFO @ Tue, 16 Jun 2020 09:37:20: 17000000 INFO @ Tue, 16 Jun 2020 09:37:22: 12000000 INFO @ Tue, 16 Jun 2020 09:37:23: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:37:23: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:37:23: #1 total tags in treatment: 17507456 INFO @ Tue, 16 Jun 2020 09:37:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:23: #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 09:37:23: #1 tags after filtering in treatment: 17507456 INFO @ Tue, 16 Jun 2020 09:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:24: #2 number of paired peaks: 168 WARNING @ Tue, 16 Jun 2020 09:37:24: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:24: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:37:24: #2 alternative fragment length(s) may be 2,23,37,521,534,597 bps INFO @ Tue, 16 Jun 2020 09:37:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:24: #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 09:37:24: #2 You may need to consider one of the other alternative d(s): 2,23,37,521,534,597 WARNING @ Tue, 16 Jun 2020 09:37:24: #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 09:37:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:28: 13000000 INFO @ Tue, 16 Jun 2020 09:37:34: 14000000 INFO @ Tue, 16 Jun 2020 09:37:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:39: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:40: 15000000 INFO @ Tue, 16 Jun 2020 09:37:46: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:52: 17000000 INFO @ Tue, 16 Jun 2020 09:37:55: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:37:55: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:37:55: #1 total tags in treatment: 17507456 INFO @ Tue, 16 Jun 2020 09:37:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:55: #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 09:37:55: #1 tags after filtering in treatment: 17507456 INFO @ Tue, 16 Jun 2020 09:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:56: #2 number of paired peaks: 168 WARNING @ Tue, 16 Jun 2020 09:37:56: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:56: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:37:56: #2 alternative fragment length(s) may be 2,23,37,521,534,597 bps INFO @ Tue, 16 Jun 2020 09:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:56: #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 09:37:56: #2 You may need to consider one of the other alternative d(s): 2,23,37,521,534,597 WARNING @ Tue, 16 Jun 2020 09:37:56: #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 09:37:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.10_summits.bed INFO @ Tue, 16 Jun 2020 09:38:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529207/SRX529207.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:36: 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。