Job ID = 6367014 SRX = SRX2582953 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:44 prefetch.2.10.7: 1) Downloading 'SRR5279129'... 2020-06-15T23:38:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:53 prefetch.2.10.7: 'SRR5279129' is valid 2020-06-15T23:40:53 prefetch.2.10.7: 1) 'SRR5279129' was downloaded successfully 2020-06-15T23:40:53 prefetch.2.10.7: 'SRR5279129' has 0 unresolved dependencies Read 15065068 spots for SRR5279129/SRR5279129.sra Written 15065068 spots for SRR5279129/SRR5279129.sra 2020-06-15T23:41:53 prefetch.2.10.7: 1) Downloading 'SRR5279130'... 2020-06-15T23:41:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:42 prefetch.2.10.7: 'SRR5279130' is valid 2020-06-15T23:45:42 prefetch.2.10.7: 1) 'SRR5279130' was downloaded successfully 2020-06-15T23:45:42 prefetch.2.10.7: 'SRR5279130' has 0 unresolved dependencies Read 14865800 spots for SRR5279130/SRR5279130.sra Written 14865800 spots for SRR5279130/SRR5279130.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: 00:06:12 29930868 reads; of these: 29930868 (100.00%) were unpaired; of these: 5849077 (19.54%) aligned 0 times 20134012 (67.27%) aligned exactly 1 time 3947779 (13.19%) aligned >1 times 80.46% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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] 6915564 / 24081791 = 0.2872 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 08:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.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 08:58:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:55: 1000000 INFO @ Tue, 16 Jun 2020 08:59:00: 2000000 INFO @ Tue, 16 Jun 2020 08:59:05: 3000000 INFO @ Tue, 16 Jun 2020 08:59:10: 4000000 INFO @ Tue, 16 Jun 2020 08:59:14: 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 08:59:19: 6000000 INFO @ Tue, 16 Jun 2020 08:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.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 08:59:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:24: 7000000 INFO @ Tue, 16 Jun 2020 08:59:26: 1000000 INFO @ Tue, 16 Jun 2020 08:59:29: 8000000 INFO @ Tue, 16 Jun 2020 08:59:31: 2000000 INFO @ Tue, 16 Jun 2020 08:59:34: 9000000 INFO @ Tue, 16 Jun 2020 08:59:37: 3000000 INFO @ Tue, 16 Jun 2020 08:59:39: 10000000 INFO @ Tue, 16 Jun 2020 08:59:42: 4000000 INFO @ Tue, 16 Jun 2020 08:59:44: 11000000 INFO @ Tue, 16 Jun 2020 08:59:48: 5000000 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 08:59:49: 12000000 INFO @ Tue, 16 Jun 2020 08:59:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.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 08:59:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:53: 6000000 INFO @ Tue, 16 Jun 2020 08:59:54: 13000000 INFO @ Tue, 16 Jun 2020 08:59:55: 1000000 INFO @ Tue, 16 Jun 2020 08:59:59: 7000000 INFO @ Tue, 16 Jun 2020 08:59:59: 14000000 INFO @ Tue, 16 Jun 2020 09:00:01: 2000000 INFO @ Tue, 16 Jun 2020 09:00:04: 8000000 INFO @ Tue, 16 Jun 2020 09:00:05: 15000000 INFO @ Tue, 16 Jun 2020 09:00:06: 3000000 INFO @ Tue, 16 Jun 2020 09:00:10: 16000000 INFO @ Tue, 16 Jun 2020 09:00:10: 9000000 INFO @ Tue, 16 Jun 2020 09:00:11: 4000000 INFO @ Tue, 16 Jun 2020 09:00:15: 17000000 INFO @ Tue, 16 Jun 2020 09:00:16: 10000000 INFO @ Tue, 16 Jun 2020 09:00:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:16: #1 total tags in treatment: 17166227 INFO @ Tue, 16 Jun 2020 09:00:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:16: #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 09:00:16: 5000000 INFO @ Tue, 16 Jun 2020 09:00:16: #1 tags after filtering in treatment: 17166227 INFO @ Tue, 16 Jun 2020 09:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:17: #2 number of paired peaks: 263 WARNING @ Tue, 16 Jun 2020 09:00:17: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:18: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:00:18: #2 alternative fragment length(s) may be 2,46,598 bps INFO @ Tue, 16 Jun 2020 09:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.05_model.r WARNING @ Tue, 16 Jun 2020 09:00:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:18: #2 You may need to consider one of the other alternative d(s): 2,46,598 WARNING @ Tue, 16 Jun 2020 09:00:18: #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 09:00:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:21: 11000000 INFO @ Tue, 16 Jun 2020 09:00:21: 6000000 INFO @ Tue, 16 Jun 2020 09:00:26: 7000000 INFO @ Tue, 16 Jun 2020 09:00:27: 12000000 INFO @ Tue, 16 Jun 2020 09:00:31: 8000000 INFO @ Tue, 16 Jun 2020 09:00:32: 13000000 INFO @ Tue, 16 Jun 2020 09:00:36: 9000000 INFO @ Tue, 16 Jun 2020 09:00:38: 14000000 INFO @ Tue, 16 Jun 2020 09:00:42: 10000000 INFO @ Tue, 16 Jun 2020 09:00:43: 15000000 INFO @ Tue, 16 Jun 2020 09:00:47: 11000000 INFO @ Tue, 16 Jun 2020 09:00:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:49: 16000000 INFO @ Tue, 16 Jun 2020 09:00:52: 12000000 INFO @ Tue, 16 Jun 2020 09:00:54: 17000000 INFO @ Tue, 16 Jun 2020 09:00:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:55: #1 total tags in treatment: 17166227 INFO @ Tue, 16 Jun 2020 09:00:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:55: #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 09:00:56: #1 tags after filtering in treatment: 17166227 INFO @ Tue, 16 Jun 2020 09:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:57: #2 number of paired peaks: 263 WARNING @ Tue, 16 Jun 2020 09:00:57: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:57: 13000000 INFO @ Tue, 16 Jun 2020 09:00:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:57: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:00:57: #2 alternative fragment length(s) may be 2,46,598 bps INFO @ Tue, 16 Jun 2020 09:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.10_model.r WARNING @ Tue, 16 Jun 2020 09:00:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:57: #2 You may need to consider one of the other alternative d(s): 2,46,598 WARNING @ Tue, 16 Jun 2020 09:00:57: #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 09:00:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:02: 14000000 INFO @ Tue, 16 Jun 2020 09:01:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.05_summits.bed INFO @ Tue, 16 Jun 2020 09:01:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:07: 15000000 INFO @ Tue, 16 Jun 2020 09:01:12: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:01:16: 17000000 INFO @ Tue, 16 Jun 2020 09:01:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:01:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:01:17: #1 total tags in treatment: 17166227 INFO @ Tue, 16 Jun 2020 09:01:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:17: #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 09:01:18: #1 tags after filtering in treatment: 17166227 INFO @ Tue, 16 Jun 2020 09:01:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:19: #2 number of paired peaks: 263 WARNING @ Tue, 16 Jun 2020 09:01:19: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:19: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:01:19: #2 alternative fragment length(s) may be 2,46,598 bps INFO @ Tue, 16 Jun 2020 09:01:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.20_model.r WARNING @ Tue, 16 Jun 2020 09:01:19: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:01:19: #2 You may need to consider one of the other alternative d(s): 2,46,598 WARNING @ Tue, 16 Jun 2020 09:01:19: #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 09:01:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.10_summits.bed INFO @ Tue, 16 Jun 2020 09:01:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (928 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582953/SRX2582953.20_summits.bed INFO @ Tue, 16 Jun 2020 09:02:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 1 millis CompletedMACS2peakCalling