Job ID = 6497432 SRX = SRX494930 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:15:30 prefetch.2.10.7: 1) Downloading 'SRR1198462'... 2020-06-25T22:15:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:18:15 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:18:15 prefetch.2.10.7: 1) 'SRR1198462' was downloaded successfully Read 23523716 spots for SRR1198462/SRR1198462.sra Written 23523716 spots for SRR1198462/SRR1198462.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: 00:05:11 23523716 reads; of these: 23523716 (100.00%) were unpaired; of these: 1170486 (4.98%) aligned 0 times 17705268 (75.27%) aligned exactly 1 time 4647962 (19.76%) aligned >1 times 95.02% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 4823027 / 22353230 = 0.2158 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 @ Fri, 26 Jun 2020 07:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.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 @ Fri, 26 Jun 2020 07:30:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:24: 1000000 INFO @ Fri, 26 Jun 2020 07:30:29: 2000000 INFO @ Fri, 26 Jun 2020 07:30:34: 3000000 INFO @ Fri, 26 Jun 2020 07:30:39: 4000000 INFO @ Fri, 26 Jun 2020 07:30:45: 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 @ Fri, 26 Jun 2020 07:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.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 @ Fri, 26 Jun 2020 07:30:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:50: 6000000 INFO @ Fri, 26 Jun 2020 07:30:55: 1000000 INFO @ Fri, 26 Jun 2020 07:30:55: 7000000 INFO @ Fri, 26 Jun 2020 07:31:00: 2000000 INFO @ Fri, 26 Jun 2020 07:31:00: 8000000 INFO @ Fri, 26 Jun 2020 07:31:05: 3000000 INFO @ Fri, 26 Jun 2020 07:31:05: 9000000 INFO @ Fri, 26 Jun 2020 07:31:11: 4000000 INFO @ Fri, 26 Jun 2020 07:31:11: 10000000 INFO @ Fri, 26 Jun 2020 07:31:16: 5000000 INFO @ Fri, 26 Jun 2020 07:31:16: 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 @ Fri, 26 Jun 2020 07:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.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 @ Fri, 26 Jun 2020 07:31:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:21: 6000000 INFO @ Fri, 26 Jun 2020 07:31:21: 12000000 INFO @ Fri, 26 Jun 2020 07:31:25: 1000000 INFO @ Fri, 26 Jun 2020 07:31:26: 7000000 INFO @ Fri, 26 Jun 2020 07:31:27: 13000000 INFO @ Fri, 26 Jun 2020 07:31:30: 2000000 INFO @ Fri, 26 Jun 2020 07:31:32: 8000000 INFO @ Fri, 26 Jun 2020 07:31:32: 14000000 INFO @ Fri, 26 Jun 2020 07:31:35: 3000000 INFO @ Fri, 26 Jun 2020 07:31:37: 9000000 INFO @ Fri, 26 Jun 2020 07:31:38: 15000000 INFO @ Fri, 26 Jun 2020 07:31:41: 4000000 INFO @ Fri, 26 Jun 2020 07:31:43: 10000000 INFO @ Fri, 26 Jun 2020 07:31:43: 16000000 INFO @ Fri, 26 Jun 2020 07:31:46: 5000000 INFO @ Fri, 26 Jun 2020 07:31:48: 11000000 INFO @ Fri, 26 Jun 2020 07:31:48: 17000000 INFO @ Fri, 26 Jun 2020 07:31:51: 6000000 INFO @ Fri, 26 Jun 2020 07:31:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:31:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:31:51: #1 total tags in treatment: 17530203 INFO @ Fri, 26 Jun 2020 07:31:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:31:52: #1 tags after filtering in treatment: 17530203 INFO @ Fri, 26 Jun 2020 07:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:53: #2 number of paired peaks: 608 WARNING @ Fri, 26 Jun 2020 07:31:53: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:53: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 07:31:53: #2 alternative fragment length(s) may be 2,58,70,88,100,117 bps INFO @ Fri, 26 Jun 2020 07:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.05_model.r WARNING @ Fri, 26 Jun 2020 07:31:53: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:53: #2 You may need to consider one of the other alternative d(s): 2,58,70,88,100,117 WARNING @ Fri, 26 Jun 2020 07:31:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:31:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:31:53: 12000000 INFO @ Fri, 26 Jun 2020 07:31:57: 7000000 INFO @ Fri, 26 Jun 2020 07:31:59: 13000000 INFO @ Fri, 26 Jun 2020 07:32:02: 8000000 INFO @ Fri, 26 Jun 2020 07:32:04: 14000000 INFO @ Fri, 26 Jun 2020 07:32:07: 9000000 INFO @ Fri, 26 Jun 2020 07:32:09: 15000000 INFO @ Fri, 26 Jun 2020 07:32:12: 10000000 INFO @ Fri, 26 Jun 2020 07:32:15: 16000000 INFO @ Fri, 26 Jun 2020 07:32:18: 11000000 INFO @ Fri, 26 Jun 2020 07:32:20: 17000000 INFO @ Fri, 26 Jun 2020 07:32:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:32:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:32:23: #1 total tags in treatment: 17530203 INFO @ Fri, 26 Jun 2020 07:32:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:32:23: 12000000 INFO @ Fri, 26 Jun 2020 07:32:23: #1 tags after filtering in treatment: 17530203 INFO @ Fri, 26 Jun 2020 07:32:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:32:23: #1 finished! INFO @ Fri, 26 Jun 2020 07:32:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:32:24: #2 number of paired peaks: 608 WARNING @ Fri, 26 Jun 2020 07:32:24: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Fri, 26 Jun 2020 07:32:24: start model_add_line... INFO @ Fri, 26 Jun 2020 07:32:25: start X-correlation... INFO @ Fri, 26 Jun 2020 07:32:25: end of X-cor INFO @ Fri, 26 Jun 2020 07:32:25: #2 finished! INFO @ Fri, 26 Jun 2020 07:32:25: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 07:32:25: #2 alternative fragment length(s) may be 2,58,70,88,100,117 bps INFO @ Fri, 26 Jun 2020 07:32:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.10_model.r WARNING @ Fri, 26 Jun 2020 07:32:25: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:32:25: #2 You may need to consider one of the other alternative d(s): 2,58,70,88,100,117 WARNING @ Fri, 26 Jun 2020 07:32:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:32:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:32:28: 13000000 INFO @ Fri, 26 Jun 2020 07:32:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:32:34: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:32:39: 15000000 INFO @ Fri, 26 Jun 2020 07:32:44: 16000000 INFO @ Fri, 26 Jun 2020 07:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.05_summits.bed INFO @ Fri, 26 Jun 2020 07:32:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1985 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:32:49: 17000000 INFO @ Fri, 26 Jun 2020 07:32:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:32:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:32:52: #1 total tags in treatment: 17530203 INFO @ Fri, 26 Jun 2020 07:32:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:32:52: #1 tags after filtering in treatment: 17530203 INFO @ Fri, 26 Jun 2020 07:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:32:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:32:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:32:53: #2 number of paired peaks: 608 WARNING @ Fri, 26 Jun 2020 07:32:53: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Fri, 26 Jun 2020 07:32:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:32:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:32:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:32:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:32:53: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 07:32:53: #2 alternative fragment length(s) may be 2,58,70,88,100,117 bps INFO @ Fri, 26 Jun 2020 07:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.20_model.r WARNING @ Fri, 26 Jun 2020 07:32:53: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:32:53: #2 You may need to consider one of the other alternative d(s): 2,58,70,88,100,117 WARNING @ Fri, 26 Jun 2020 07:32:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:32:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.10_summits.bed INFO @ Fri, 26 Jun 2020 07:33:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:33:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494930/SRX494930.20_summits.bed INFO @ Fri, 26 Jun 2020 07:33:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 1 millis CompletedMACS2peakCalling