Job ID = 6368006 SRX = SRX466469 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:57:12 prefetch.2.10.7: 1) Downloading 'SRR1163535'... 2020-06-15T23:57:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:59:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:59:52 prefetch.2.10.7: 1) 'SRR1163535' was downloaded successfully Read 38123596 spots for SRR1163535/SRR1163535.sra Written 38123596 spots for SRR1163535/SRR1163535.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: 00:09:06 38123596 reads; of these: 38123596 (100.00%) were unpaired; of these: 1262960 (3.31%) aligned 0 times 30408063 (79.76%) aligned exactly 1 time 6452573 (16.93%) aligned >1 times 96.69% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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] 18267756 / 36860636 = 0.4956 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 09:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.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 09:18:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:57: 1000000 INFO @ Tue, 16 Jun 2020 09:19:02: 2000000 INFO @ Tue, 16 Jun 2020 09:19:07: 3000000 INFO @ Tue, 16 Jun 2020 09:19:12: 4000000 INFO @ Tue, 16 Jun 2020 09:19:16: 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 09:19:21: 6000000 INFO @ Tue, 16 Jun 2020 09:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.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 09:19:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:26: 7000000 INFO @ Tue, 16 Jun 2020 09:19:28: 1000000 INFO @ Tue, 16 Jun 2020 09:19:31: 8000000 INFO @ Tue, 16 Jun 2020 09:19:33: 2000000 INFO @ Tue, 16 Jun 2020 09:19:36: 9000000 INFO @ Tue, 16 Jun 2020 09:19:38: 3000000 INFO @ Tue, 16 Jun 2020 09:19:41: 10000000 INFO @ Tue, 16 Jun 2020 09:19:43: 4000000 INFO @ Tue, 16 Jun 2020 09:19:46: 11000000 INFO @ Tue, 16 Jun 2020 09:19:48: 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 09:19:51: 12000000 INFO @ Tue, 16 Jun 2020 09:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.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 09:19:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:53: 6000000 INFO @ Tue, 16 Jun 2020 09:19:56: 13000000 INFO @ Tue, 16 Jun 2020 09:19:58: 1000000 INFO @ Tue, 16 Jun 2020 09:19:58: 7000000 INFO @ Tue, 16 Jun 2020 09:20:02: 14000000 INFO @ Tue, 16 Jun 2020 09:20:03: 2000000 INFO @ Tue, 16 Jun 2020 09:20:03: 8000000 INFO @ Tue, 16 Jun 2020 09:20:07: 15000000 INFO @ Tue, 16 Jun 2020 09:20:08: 3000000 INFO @ Tue, 16 Jun 2020 09:20:08: 9000000 INFO @ Tue, 16 Jun 2020 09:20:12: 16000000 INFO @ Tue, 16 Jun 2020 09:20:13: 4000000 INFO @ Tue, 16 Jun 2020 09:20:13: 10000000 INFO @ Tue, 16 Jun 2020 09:20:17: 17000000 INFO @ Tue, 16 Jun 2020 09:20:18: 5000000 INFO @ Tue, 16 Jun 2020 09:20:19: 11000000 INFO @ Tue, 16 Jun 2020 09:20:22: 18000000 INFO @ Tue, 16 Jun 2020 09:20:23: 6000000 INFO @ Tue, 16 Jun 2020 09:20:24: 12000000 INFO @ Tue, 16 Jun 2020 09:20:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:25: #1 total tags in treatment: 18592880 INFO @ Tue, 16 Jun 2020 09:20:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:25: #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 09:20:26: #1 tags after filtering in treatment: 18592880 INFO @ Tue, 16 Jun 2020 09:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:27: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 09:20:27: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:27: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:20:27: #2 alternative fragment length(s) may be 1,46,538 bps INFO @ Tue, 16 Jun 2020 09:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:27: #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 09:20:27: #2 You may need to consider one of the other alternative d(s): 1,46,538 WARNING @ Tue, 16 Jun 2020 09:20:27: #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 09:20:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:29: 7000000 INFO @ Tue, 16 Jun 2020 09:20:29: 13000000 INFO @ Tue, 16 Jun 2020 09:20:34: 8000000 INFO @ Tue, 16 Jun 2020 09:20:34: 14000000 INFO @ Tue, 16 Jun 2020 09:20:39: 9000000 INFO @ Tue, 16 Jun 2020 09:20:40: 15000000 INFO @ Tue, 16 Jun 2020 09:20:45: 10000000 INFO @ Tue, 16 Jun 2020 09:20:45: 16000000 INFO @ Tue, 16 Jun 2020 09:20:50: 11000000 INFO @ Tue, 16 Jun 2020 09:20:50: 17000000 INFO @ Tue, 16 Jun 2020 09:20:55: 12000000 INFO @ Tue, 16 Jun 2020 09:20:56: 18000000 INFO @ Tue, 16 Jun 2020 09:20:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:59: #1 total tags in treatment: 18592880 INFO @ Tue, 16 Jun 2020 09:20:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:59: #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 09:20:59: #1 tags after filtering in treatment: 18592880 INFO @ Tue, 16 Jun 2020 09:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:00: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 09:21:00: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:01: 13000000 INFO @ Tue, 16 Jun 2020 09:21:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:01: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:21:01: #2 alternative fragment length(s) may be 1,46,538 bps INFO @ Tue, 16 Jun 2020 09:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:01: #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 09:21:01: #2 You may need to consider one of the other alternative d(s): 1,46,538 WARNING @ Tue, 16 Jun 2020 09:21:01: #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 09:21:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:06: 14000000 INFO @ Tue, 16 Jun 2020 09:21:11: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:16: 16000000 INFO @ Tue, 16 Jun 2020 09:21:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1577 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:22: 17000000 INFO @ Tue, 16 Jun 2020 09:21:27: 18000000 INFO @ Tue, 16 Jun 2020 09:21:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:30: #1 total tags in treatment: 18592880 INFO @ Tue, 16 Jun 2020 09:21:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:30: #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 09:21:30: #1 tags after filtering in treatment: 18592880 INFO @ Tue, 16 Jun 2020 09:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:32: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 09:21:32: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:32: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:21:32: #2 alternative fragment length(s) may be 1,46,538 bps INFO @ Tue, 16 Jun 2020 09:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:32: #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 09:21:32: #2 You may need to consider one of the other alternative d(s): 1,46,538 WARNING @ Tue, 16 Jun 2020 09:21:32: #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 09:21:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466469/SRX466469.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling