Job ID = 6368034 SRX = SRX466497 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:02:15 prefetch.2.10.7: 1) Downloading 'SRR1163563'... 2020-06-16T00:02:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:37 prefetch.2.10.7: 1) 'SRR1163563' was downloaded successfully Read 31990085 spots for SRR1163563/SRR1163563.sra Written 31990085 spots for SRR1163563/SRR1163563.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: 00:08:53 31990085 reads; of these: 31990085 (100.00%) were unpaired; of these: 1352262 (4.23%) aligned 0 times 20560313 (64.27%) aligned exactly 1 time 10077510 (31.50%) aligned >1 times 95.77% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 14060406 / 30637823 = 0.4589 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 09:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.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 09:22:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:46: 1000000 INFO @ Tue, 16 Jun 2020 09:22:52: 2000000 INFO @ Tue, 16 Jun 2020 09:22:58: 3000000 INFO @ Tue, 16 Jun 2020 09:23:04: 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 09:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.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 09:23:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:10: 5000000 INFO @ Tue, 16 Jun 2020 09:23:18: 6000000 INFO @ Tue, 16 Jun 2020 09:23:19: 1000000 INFO @ Tue, 16 Jun 2020 09:23:26: 7000000 INFO @ Tue, 16 Jun 2020 09:23:27: 2000000 INFO @ Tue, 16 Jun 2020 09:23:33: 8000000 INFO @ Tue, 16 Jun 2020 09:23:36: 3000000 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 09:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.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 09:23:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:41: 9000000 INFO @ Tue, 16 Jun 2020 09:23:45: 4000000 INFO @ Tue, 16 Jun 2020 09:23:47: 1000000 INFO @ Tue, 16 Jun 2020 09:23:49: 10000000 INFO @ Tue, 16 Jun 2020 09:23:54: 5000000 INFO @ Tue, 16 Jun 2020 09:23:55: 2000000 INFO @ Tue, 16 Jun 2020 09:23:56: 11000000 INFO @ Tue, 16 Jun 2020 09:24:02: 6000000 INFO @ Tue, 16 Jun 2020 09:24:03: 3000000 INFO @ Tue, 16 Jun 2020 09:24:04: 12000000 INFO @ Tue, 16 Jun 2020 09:24:11: 7000000 INFO @ Tue, 16 Jun 2020 09:24:11: 4000000 INFO @ Tue, 16 Jun 2020 09:24:12: 13000000 INFO @ Tue, 16 Jun 2020 09:24:19: 5000000 INFO @ Tue, 16 Jun 2020 09:24:19: 8000000 INFO @ Tue, 16 Jun 2020 09:24:20: 14000000 INFO @ Tue, 16 Jun 2020 09:24:26: 6000000 INFO @ Tue, 16 Jun 2020 09:24:27: 15000000 INFO @ Tue, 16 Jun 2020 09:24:28: 9000000 INFO @ Tue, 16 Jun 2020 09:24:34: 7000000 INFO @ Tue, 16 Jun 2020 09:24:35: 16000000 INFO @ Tue, 16 Jun 2020 09:24:36: 10000000 INFO @ Tue, 16 Jun 2020 09:24:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:24:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:24:40: #1 total tags in treatment: 16577417 INFO @ Tue, 16 Jun 2020 09:24:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:40: #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 09:24:40: #1 tags after filtering in treatment: 16577417 INFO @ Tue, 16 Jun 2020 09:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:41: #2 number of paired peaks: 1241 INFO @ Tue, 16 Jun 2020 09:24:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:41: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:24:41: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:41: #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 09:24:41: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:24:41: #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 09:24:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:42: 8000000 INFO @ Tue, 16 Jun 2020 09:24:45: 11000000 INFO @ Tue, 16 Jun 2020 09:24:50: 9000000 INFO @ Tue, 16 Jun 2020 09:24:53: 12000000 INFO @ Tue, 16 Jun 2020 09:24:57: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:02: 13000000 INFO @ Tue, 16 Jun 2020 09:25:05: 11000000 INFO @ Tue, 16 Jun 2020 09:25:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:10: 14000000 INFO @ Tue, 16 Jun 2020 09:25:13: 12000000 INFO @ Tue, 16 Jun 2020 09:25:18: 15000000 INFO @ Tue, 16 Jun 2020 09:25:20: 13000000 INFO @ Tue, 16 Jun 2020 09:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:26: 16000000 INFO @ Tue, 16 Jun 2020 09:25:28: 14000000 INFO @ Tue, 16 Jun 2020 09:25:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:31: #1 total tags in treatment: 16577417 INFO @ Tue, 16 Jun 2020 09:25:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:31: #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 09:25:31: #1 tags after filtering in treatment: 16577417 INFO @ Tue, 16 Jun 2020 09:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:33: #2 number of paired peaks: 1241 INFO @ Tue, 16 Jun 2020 09:25:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:33: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:25:33: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.10_model.r WARNING @ Tue, 16 Jun 2020 09:25:33: #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 09:25:33: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:25:33: #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 09:25:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:35: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:25:41: 16000000 INFO @ Tue, 16 Jun 2020 09:25:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:45: #1 total tags in treatment: 16577417 INFO @ Tue, 16 Jun 2020 09:25:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:45: #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 09:25:45: #1 tags after filtering in treatment: 16577417 INFO @ Tue, 16 Jun 2020 09:25:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:46: #2 number of paired peaks: 1241 INFO @ Tue, 16 Jun 2020 09:25:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:47: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:25:47: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:25:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.20_model.r WARNING @ Tue, 16 Jun 2020 09:25:47: #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 09:25:47: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:25:47: #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 09:25:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:12: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466497/SRX466497.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:26: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling