Job ID = 6366263 SRX = SRX1007135 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:52 prefetch.2.10.7: 1) Downloading 'SRR1993095'... 2020-06-15T22:43:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:47 prefetch.2.10.7: 1) 'SRR1993095' was downloaded successfully Read 44398214 spots for SRR1993095/SRR1993095.sra Written 44398214 spots for SRR1993095/SRR1993095.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: 00:06:48 44398214 reads; of these: 44398214 (100.00%) were unpaired; of these: 11214538 (25.26%) aligned 0 times 28085330 (63.26%) aligned exactly 1 time 5098346 (11.48%) aligned >1 times 74.74% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 8842102 / 33183676 = 0.2665 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 08:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.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 08:03:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:52: 1000000 INFO @ Tue, 16 Jun 2020 08:03:57: 2000000 INFO @ Tue, 16 Jun 2020 08:04:02: 3000000 INFO @ Tue, 16 Jun 2020 08:04:07: 4000000 INFO @ Tue, 16 Jun 2020 08:04:12: 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 08:04:17: 6000000 INFO @ Tue, 16 Jun 2020 08:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.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 08:04:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:22: 7000000 INFO @ Tue, 16 Jun 2020 08:04:22: 1000000 INFO @ Tue, 16 Jun 2020 08:04:27: 2000000 INFO @ Tue, 16 Jun 2020 08:04:28: 8000000 INFO @ Tue, 16 Jun 2020 08:04:32: 3000000 INFO @ Tue, 16 Jun 2020 08:04:33: 9000000 INFO @ Tue, 16 Jun 2020 08:04:38: 4000000 INFO @ Tue, 16 Jun 2020 08:04:38: 10000000 INFO @ Tue, 16 Jun 2020 08:04:43: 5000000 INFO @ Tue, 16 Jun 2020 08:04:43: 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 08:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.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 08:04:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:48: 6000000 INFO @ Tue, 16 Jun 2020 08:04:49: 12000000 INFO @ Tue, 16 Jun 2020 08:04:53: 1000000 INFO @ Tue, 16 Jun 2020 08:04:53: 7000000 INFO @ Tue, 16 Jun 2020 08:04:54: 13000000 INFO @ Tue, 16 Jun 2020 08:04:58: 2000000 INFO @ Tue, 16 Jun 2020 08:04:58: 8000000 INFO @ Tue, 16 Jun 2020 08:04:59: 14000000 INFO @ Tue, 16 Jun 2020 08:05:03: 3000000 INFO @ Tue, 16 Jun 2020 08:05:03: 9000000 INFO @ Tue, 16 Jun 2020 08:05:05: 15000000 INFO @ Tue, 16 Jun 2020 08:05:08: 4000000 INFO @ Tue, 16 Jun 2020 08:05:09: 10000000 INFO @ Tue, 16 Jun 2020 08:05:10: 16000000 INFO @ Tue, 16 Jun 2020 08:05:14: 5000000 INFO @ Tue, 16 Jun 2020 08:05:14: 11000000 INFO @ Tue, 16 Jun 2020 08:05:16: 17000000 INFO @ Tue, 16 Jun 2020 08:05:19: 6000000 INFO @ Tue, 16 Jun 2020 08:05:20: 12000000 INFO @ Tue, 16 Jun 2020 08:05:21: 18000000 INFO @ Tue, 16 Jun 2020 08:05:24: 7000000 INFO @ Tue, 16 Jun 2020 08:05:25: 13000000 INFO @ Tue, 16 Jun 2020 08:05:26: 19000000 INFO @ Tue, 16 Jun 2020 08:05:30: 8000000 INFO @ Tue, 16 Jun 2020 08:05:31: 14000000 INFO @ Tue, 16 Jun 2020 08:05:32: 20000000 INFO @ Tue, 16 Jun 2020 08:05:35: 9000000 INFO @ Tue, 16 Jun 2020 08:05:37: 21000000 INFO @ Tue, 16 Jun 2020 08:05:37: 15000000 INFO @ Tue, 16 Jun 2020 08:05:40: 10000000 INFO @ Tue, 16 Jun 2020 08:05:42: 22000000 INFO @ Tue, 16 Jun 2020 08:05:43: 16000000 INFO @ Tue, 16 Jun 2020 08:05:45: 11000000 INFO @ Tue, 16 Jun 2020 08:05:48: 23000000 INFO @ Tue, 16 Jun 2020 08:05:48: 17000000 INFO @ Tue, 16 Jun 2020 08:05:51: 12000000 INFO @ Tue, 16 Jun 2020 08:05:53: 24000000 INFO @ Tue, 16 Jun 2020 08:05:54: 18000000 INFO @ Tue, 16 Jun 2020 08:05:55: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:05:55: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:05:55: #1 total tags in treatment: 24341574 INFO @ Tue, 16 Jun 2020 08:05:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:55: #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 08:05:56: #1 tags after filtering in treatment: 24341574 INFO @ Tue, 16 Jun 2020 08:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:56: 13000000 INFO @ Tue, 16 Jun 2020 08:05:57: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 08:05:57: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:58: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:05:58: #2 alternative fragment length(s) may be 2,42,571 bps INFO @ Tue, 16 Jun 2020 08:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.05_model.r WARNING @ Tue, 16 Jun 2020 08:05:58: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:58: #2 You may need to consider one of the other alternative d(s): 2,42,571 WARNING @ Tue, 16 Jun 2020 08:05:58: #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 08:05:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:00: 19000000 INFO @ Tue, 16 Jun 2020 08:06:01: 14000000 INFO @ Tue, 16 Jun 2020 08:06:05: 20000000 INFO @ Tue, 16 Jun 2020 08:06:07: 15000000 INFO @ Tue, 16 Jun 2020 08:06:11: 21000000 INFO @ Tue, 16 Jun 2020 08:06:12: 16000000 INFO @ Tue, 16 Jun 2020 08:06:16: 22000000 INFO @ Tue, 16 Jun 2020 08:06:17: 17000000 INFO @ Tue, 16 Jun 2020 08:06:22: 23000000 INFO @ Tue, 16 Jun 2020 08:06:22: 18000000 INFO @ Tue, 16 Jun 2020 08:06:27: 24000000 INFO @ Tue, 16 Jun 2020 08:06:27: 19000000 INFO @ Tue, 16 Jun 2020 08:06:29: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:06:29: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:06:29: #1 total tags in treatment: 24341574 INFO @ Tue, 16 Jun 2020 08:06:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:29: #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 08:06:30: #1 tags after filtering in treatment: 24341574 INFO @ Tue, 16 Jun 2020 08:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:31: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 08:06:31: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:32: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:06:32: #2 alternative fragment length(s) may be 2,42,571 bps INFO @ Tue, 16 Jun 2020 08:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:32: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:32: #2 You may need to consider one of the other alternative d(s): 2,42,571 WARNING @ Tue, 16 Jun 2020 08:06:32: #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 08:06:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:33: 20000000 INFO @ Tue, 16 Jun 2020 08:06:38: 21000000 INFO @ Tue, 16 Jun 2020 08:06:43: 22000000 INFO @ Tue, 16 Jun 2020 08:06:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:48: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:53: 24000000 INFO @ Tue, 16 Jun 2020 08:06:55: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:06:55: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:06:55: #1 total tags in treatment: 24341574 INFO @ Tue, 16 Jun 2020 08:06:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:55: #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 08:06:56: #1 tags after filtering in treatment: 24341574 INFO @ Tue, 16 Jun 2020 08:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:57: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 08:06:57: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:58: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2 alternative fragment length(s) may be 2,42,571 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:58: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:58: #2 You may need to consider one of the other alternative d(s): 2,42,571 WARNING @ Tue, 16 Jun 2020 08:06:58: #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 08:06:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:11: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (12677 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6268 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1007135/SRX1007135.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1988 records, 4 fields): 4 millis CompletedMACS2peakCalling