Job ID = 6366264 SRX = SRX1007136 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:41:21 prefetch.2.10.7: 1) Downloading 'SRR1993096'... 2020-06-15T22:41:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:47 prefetch.2.10.7: 1) 'SRR1993096' was downloaded successfully Read 34711485 spots for SRR1993096/SRR1993096.sra Written 34711485 spots for SRR1993096/SRR1993096.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: 00:05:46 34711485 reads; of these: 34711485 (100.00%) were unpaired; of these: 7206089 (20.76%) aligned 0 times 23779659 (68.51%) aligned exactly 1 time 3725737 (10.73%) aligned >1 times 79.24% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 6835428 / 27505396 = 0.2485 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 07:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.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 07:57:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:12: 1000000 INFO @ Tue, 16 Jun 2020 07:57:18: 2000000 INFO @ Tue, 16 Jun 2020 07:57:23: 3000000 INFO @ Tue, 16 Jun 2020 07:57:29: 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 07:57:35: 5000000 INFO @ Tue, 16 Jun 2020 07:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.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 07:57:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:41: 6000000 INFO @ Tue, 16 Jun 2020 07:57:43: 1000000 INFO @ Tue, 16 Jun 2020 07:57:47: 7000000 INFO @ Tue, 16 Jun 2020 07:57:50: 2000000 INFO @ Tue, 16 Jun 2020 07:57:54: 8000000 INFO @ Tue, 16 Jun 2020 07:57:56: 3000000 INFO @ Tue, 16 Jun 2020 07:58:01: 9000000 INFO @ Tue, 16 Jun 2020 07:58:03: 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 07:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.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 07:58:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:07: 10000000 INFO @ Tue, 16 Jun 2020 07:58:10: 5000000 INFO @ Tue, 16 Jun 2020 07:58:13: 1000000 INFO @ Tue, 16 Jun 2020 07:58:14: 11000000 INFO @ Tue, 16 Jun 2020 07:58:17: 6000000 INFO @ Tue, 16 Jun 2020 07:58:20: 2000000 INFO @ Tue, 16 Jun 2020 07:58:20: 12000000 INFO @ Tue, 16 Jun 2020 07:58:24: 7000000 INFO @ Tue, 16 Jun 2020 07:58:27: 3000000 INFO @ Tue, 16 Jun 2020 07:58:27: 13000000 INFO @ Tue, 16 Jun 2020 07:58:30: 8000000 INFO @ Tue, 16 Jun 2020 07:58:34: 14000000 INFO @ Tue, 16 Jun 2020 07:58:34: 4000000 INFO @ Tue, 16 Jun 2020 07:58:37: 9000000 INFO @ Tue, 16 Jun 2020 07:58:40: 15000000 INFO @ Tue, 16 Jun 2020 07:58:41: 5000000 INFO @ Tue, 16 Jun 2020 07:58:44: 10000000 INFO @ Tue, 16 Jun 2020 07:58:47: 16000000 INFO @ Tue, 16 Jun 2020 07:58:48: 6000000 INFO @ Tue, 16 Jun 2020 07:58:50: 11000000 INFO @ Tue, 16 Jun 2020 07:58:54: 17000000 INFO @ Tue, 16 Jun 2020 07:58:55: 7000000 INFO @ Tue, 16 Jun 2020 07:58:57: 12000000 INFO @ Tue, 16 Jun 2020 07:59:00: 18000000 INFO @ Tue, 16 Jun 2020 07:59:02: 8000000 INFO @ Tue, 16 Jun 2020 07:59:04: 13000000 INFO @ Tue, 16 Jun 2020 07:59:07: 19000000 INFO @ Tue, 16 Jun 2020 07:59:09: 9000000 INFO @ Tue, 16 Jun 2020 07:59:10: 14000000 INFO @ Tue, 16 Jun 2020 07:59:14: 20000000 INFO @ Tue, 16 Jun 2020 07:59:16: 10000000 INFO @ Tue, 16 Jun 2020 07:59:17: 15000000 INFO @ Tue, 16 Jun 2020 07:59:18: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:59:18: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:59:18: #1 total tags in treatment: 20669968 INFO @ Tue, 16 Jun 2020 07:59:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:18: #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 07:59:19: #1 tags after filtering in treatment: 20669968 INFO @ Tue, 16 Jun 2020 07:59:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:20: #2 number of paired peaks: 904 WARNING @ Tue, 16 Jun 2020 07:59:20: Fewer paired peaks (904) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 904 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:20: #2 predicted fragment length is 62 bps INFO @ Tue, 16 Jun 2020 07:59:20: #2 alternative fragment length(s) may be 3,62 bps INFO @ Tue, 16 Jun 2020 07:59:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.05_model.r WARNING @ Tue, 16 Jun 2020 07:59:20: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:20: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Tue, 16 Jun 2020 07:59:20: #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 07:59:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:22: 11000000 INFO @ Tue, 16 Jun 2020 07:59:24: 16000000 INFO @ Tue, 16 Jun 2020 07:59:29: 12000000 INFO @ Tue, 16 Jun 2020 07:59:31: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:59:36: 13000000 INFO @ Tue, 16 Jun 2020 07:59:38: 18000000 INFO @ Tue, 16 Jun 2020 07:59:42: 14000000 INFO @ Tue, 16 Jun 2020 07:59:45: 19000000 INFO @ Tue, 16 Jun 2020 07:59:49: 15000000 INFO @ Tue, 16 Jun 2020 07:59:51: 20000000 INFO @ Tue, 16 Jun 2020 07:59:56: 16000000 INFO @ Tue, 16 Jun 2020 07:59:56: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 07:59:56: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 07:59:56: #1 total tags in treatment: 20669968 INFO @ Tue, 16 Jun 2020 07:59:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:56: #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 07:59:56: #1 tags after filtering in treatment: 20669968 INFO @ Tue, 16 Jun 2020 07:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:58: #2 number of paired peaks: 904 WARNING @ Tue, 16 Jun 2020 07:59:58: Fewer paired peaks (904) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 904 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:58: #2 predicted fragment length is 62 bps INFO @ Tue, 16 Jun 2020 07:59:58: #2 alternative fragment length(s) may be 3,62 bps INFO @ Tue, 16 Jun 2020 07:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.10_model.r WARNING @ Tue, 16 Jun 2020 07:59:58: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:59:58: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Tue, 16 Jun 2020 07:59:58: #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 07:59:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:02: 17000000 INFO @ Tue, 16 Jun 2020 08:00:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:09: 18000000 INFO @ Tue, 16 Jun 2020 08:00:15: 19000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:22: 20000000 INFO @ Tue, 16 Jun 2020 08:00:26: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:00:26: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:00:26: #1 total tags in treatment: 20669968 INFO @ Tue, 16 Jun 2020 08:00:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:26: #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 08:00:26: #1 tags after filtering in treatment: 20669968 INFO @ Tue, 16 Jun 2020 08:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:28: #2 number of paired peaks: 904 WARNING @ Tue, 16 Jun 2020 08:00:28: Fewer paired peaks (904) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 904 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:28: #2 predicted fragment length is 62 bps INFO @ Tue, 16 Jun 2020 08:00:28: #2 alternative fragment length(s) may be 3,62 bps INFO @ Tue, 16 Jun 2020 08:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.20_model.r WARNING @ Tue, 16 Jun 2020 08:00:28: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:00:28: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Tue, 16 Jun 2020 08:00:28: #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 08:00:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.05_summits.bed INFO @ Tue, 16 Jun 2020 08:00:28: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (15702 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8526 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007136/SRX1007136.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3920 records, 4 fields): 5 millis CompletedMACS2peakCalling