Job ID = 6368042 SRX = SRX466505 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:49:18 prefetch.2.10.7: 1) Downloading 'SRR1163571'... 2020-06-15T23:49:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:52 prefetch.2.10.7: 1) 'SRR1163571' was downloaded successfully Read 16287635 spots for SRR1163571/SRR1163571.sra Written 16287635 spots for SRR1163571/SRR1163571.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: 00:03:08 16287635 reads; of these: 16287635 (100.00%) were unpaired; of these: 229461 (1.41%) aligned 0 times 13726292 (84.27%) aligned exactly 1 time 2331882 (14.32%) aligned >1 times 98.59% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 3074835 / 16058174 = 0.1915 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 09:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.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 09:00:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:03: 1000000 INFO @ Tue, 16 Jun 2020 09:01:08: 2000000 INFO @ Tue, 16 Jun 2020 09:01:13: 3000000 INFO @ Tue, 16 Jun 2020 09:01:19: 4000000 INFO @ Tue, 16 Jun 2020 09:01:24: 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 09:01:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.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 09:01:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:29: 6000000 INFO @ Tue, 16 Jun 2020 09:01:33: 1000000 INFO @ Tue, 16 Jun 2020 09:01:34: 7000000 INFO @ Tue, 16 Jun 2020 09:01:38: 2000000 INFO @ Tue, 16 Jun 2020 09:01:39: 8000000 INFO @ Tue, 16 Jun 2020 09:01:43: 3000000 INFO @ Tue, 16 Jun 2020 09:01:45: 9000000 INFO @ Tue, 16 Jun 2020 09:01:48: 4000000 INFO @ Tue, 16 Jun 2020 09:01:50: 10000000 INFO @ Tue, 16 Jun 2020 09:01:53: 5000000 INFO @ Tue, 16 Jun 2020 09:01:55: 11000000 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 09:01:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.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 09:01:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:59: 6000000 INFO @ Tue, 16 Jun 2020 09:02:00: 12000000 INFO @ Tue, 16 Jun 2020 09:02:03: 1000000 INFO @ Tue, 16 Jun 2020 09:02:04: 7000000 INFO @ Tue, 16 Jun 2020 09:02:06: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:02:06: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:02:06: #1 total tags in treatment: 12983339 INFO @ Tue, 16 Jun 2020 09:02:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:06: #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 09:02:06: #1 tags after filtering in treatment: 12983339 INFO @ Tue, 16 Jun 2020 09:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:07: #2 number of paired peaks: 207 WARNING @ Tue, 16 Jun 2020 09:02:07: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:07: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:02:07: #2 alternative fragment length(s) may be 2,48,262,537 bps INFO @ Tue, 16 Jun 2020 09:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:07: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:07: #2 You may need to consider one of the other alternative d(s): 2,48,262,537 WARNING @ Tue, 16 Jun 2020 09:02:07: #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 09:02:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:09: 8000000 INFO @ Tue, 16 Jun 2020 09:02:10: 2000000 INFO @ Tue, 16 Jun 2020 09:02:15: 9000000 INFO @ Tue, 16 Jun 2020 09:02:16: 3000000 INFO @ Tue, 16 Jun 2020 09:02:20: 10000000 INFO @ Tue, 16 Jun 2020 09:02:22: 4000000 INFO @ Tue, 16 Jun 2020 09:02:25: 11000000 INFO @ Tue, 16 Jun 2020 09:02:28: 5000000 INFO @ Tue, 16 Jun 2020 09:02:31: 12000000 INFO @ Tue, 16 Jun 2020 09:02:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:34: 6000000 INFO @ Tue, 16 Jun 2020 09:02:36: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:02:36: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:02:36: #1 total tags in treatment: 12983339 INFO @ Tue, 16 Jun 2020 09:02:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:36: #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 09:02:36: #1 tags after filtering in treatment: 12983339 INFO @ Tue, 16 Jun 2020 09:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:37: #2 number of paired peaks: 207 WARNING @ Tue, 16 Jun 2020 09:02:37: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:37: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:02:37: #2 alternative fragment length(s) may be 2,48,262,537 bps INFO @ Tue, 16 Jun 2020 09:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.10_model.r WARNING @ Tue, 16 Jun 2020 09:02:37: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:37: #2 You may need to consider one of the other alternative d(s): 2,48,262,537 WARNING @ Tue, 16 Jun 2020 09:02:37: #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 09:02:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:40: 7000000 INFO @ Tue, 16 Jun 2020 09:02:46: 8000000 INFO @ Tue, 16 Jun 2020 09:02:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:52: 9000000 INFO @ Tue, 16 Jun 2020 09:02:58: 10000000 INFO @ Tue, 16 Jun 2020 09:03:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:04: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:10: 12000000 INFO @ Tue, 16 Jun 2020 09:03:16: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:03:16: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:03:16: #1 total tags in treatment: 12983339 INFO @ Tue, 16 Jun 2020 09:03:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:16: #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 09:03:16: #1 tags after filtering in treatment: 12983339 INFO @ Tue, 16 Jun 2020 09:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:17: #2 number of paired peaks: 207 WARNING @ Tue, 16 Jun 2020 09:03:17: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:17: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:03:17: #2 alternative fragment length(s) may be 2,48,262,537 bps INFO @ Tue, 16 Jun 2020 09:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:17: #2 You may need to consider one of the other alternative d(s): 2,48,262,537 WARNING @ Tue, 16 Jun 2020 09:03:17: #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 09:03:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:03:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466505/SRX466505.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (95 records, 4 fields): 3 millis CompletedMACS2peakCalling