Job ID = 6366561 SRX = SRX1936239 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:56 prefetch.2.10.7: 1) Downloading 'SRR3879846'... 2020-06-15T22:51:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:56 prefetch.2.10.7: 1) 'SRR3879846' was downloaded successfully Read 23727403 spots for SRR3879846/SRR3879846.sra Written 23727403 spots for SRR3879846/SRR3879846.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: 00:05:49 23727403 reads; of these: 23727403 (100.00%) were unpaired; of these: 788889 (3.32%) aligned 0 times 19505222 (82.21%) aligned exactly 1 time 3433292 (14.47%) aligned >1 times 96.68% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 3215022 / 22938514 = 0.1402 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 08:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.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 08:06:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:58: 1000000 INFO @ Tue, 16 Jun 2020 08:07:04: 2000000 INFO @ Tue, 16 Jun 2020 08:07:10: 3000000 INFO @ Tue, 16 Jun 2020 08:07:16: 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 08:07:21: 5000000 INFO @ Tue, 16 Jun 2020 08:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.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 08:07:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:27: 6000000 INFO @ Tue, 16 Jun 2020 08:07:29: 1000000 INFO @ Tue, 16 Jun 2020 08:07:33: 7000000 INFO @ Tue, 16 Jun 2020 08:07:35: 2000000 INFO @ Tue, 16 Jun 2020 08:07:39: 8000000 INFO @ Tue, 16 Jun 2020 08:07:41: 3000000 INFO @ Tue, 16 Jun 2020 08:07:45: 9000000 INFO @ Tue, 16 Jun 2020 08:07:47: 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 08:07:51: 10000000 INFO @ Tue, 16 Jun 2020 08:07:53: 5000000 INFO @ Tue, 16 Jun 2020 08:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.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 08:07:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:57: 11000000 INFO @ Tue, 16 Jun 2020 08:07:59: 6000000 INFO @ Tue, 16 Jun 2020 08:07:59: 1000000 INFO @ Tue, 16 Jun 2020 08:08:03: 12000000 INFO @ Tue, 16 Jun 2020 08:08:05: 7000000 INFO @ Tue, 16 Jun 2020 08:08:05: 2000000 INFO @ Tue, 16 Jun 2020 08:08:10: 13000000 INFO @ Tue, 16 Jun 2020 08:08:11: 8000000 INFO @ Tue, 16 Jun 2020 08:08:12: 3000000 INFO @ Tue, 16 Jun 2020 08:08:16: 14000000 INFO @ Tue, 16 Jun 2020 08:08:17: 9000000 INFO @ Tue, 16 Jun 2020 08:08:18: 4000000 INFO @ Tue, 16 Jun 2020 08:08:22: 15000000 INFO @ Tue, 16 Jun 2020 08:08:23: 10000000 INFO @ Tue, 16 Jun 2020 08:08:24: 5000000 INFO @ Tue, 16 Jun 2020 08:08:28: 16000000 INFO @ Tue, 16 Jun 2020 08:08:29: 11000000 INFO @ Tue, 16 Jun 2020 08:08:30: 6000000 INFO @ Tue, 16 Jun 2020 08:08:34: 17000000 INFO @ Tue, 16 Jun 2020 08:08:36: 12000000 INFO @ Tue, 16 Jun 2020 08:08:36: 7000000 INFO @ Tue, 16 Jun 2020 08:08:41: 18000000 INFO @ Tue, 16 Jun 2020 08:08:42: 13000000 INFO @ Tue, 16 Jun 2020 08:08:42: 8000000 INFO @ Tue, 16 Jun 2020 08:08:47: 19000000 INFO @ Tue, 16 Jun 2020 08:08:48: 14000000 INFO @ Tue, 16 Jun 2020 08:08:48: 9000000 INFO @ Tue, 16 Jun 2020 08:08:51: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:08:51: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:08:51: #1 total tags in treatment: 19723492 INFO @ Tue, 16 Jun 2020 08:08:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:51: #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 08:08:51: #1 tags after filtering in treatment: 19723492 INFO @ Tue, 16 Jun 2020 08:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:53: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 08:08:53: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:53: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:08:53: #2 alternative fragment length(s) may be 1,47 bps INFO @ Tue, 16 Jun 2020 08:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:53: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Tue, 16 Jun 2020 08:08:53: #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 08:08:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:54: 15000000 INFO @ Tue, 16 Jun 2020 08:08:54: 10000000 INFO @ Tue, 16 Jun 2020 08:09:00: 16000000 INFO @ Tue, 16 Jun 2020 08:09:00: 11000000 INFO @ Tue, 16 Jun 2020 08:09:06: 17000000 INFO @ Tue, 16 Jun 2020 08:09:06: 12000000 INFO @ Tue, 16 Jun 2020 08:09:12: 18000000 INFO @ Tue, 16 Jun 2020 08:09:12: 13000000 INFO @ Tue, 16 Jun 2020 08:09:18: 19000000 INFO @ Tue, 16 Jun 2020 08:09:18: 14000000 INFO @ Tue, 16 Jun 2020 08:09:22: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:09:22: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:09:22: #1 total tags in treatment: 19723492 INFO @ Tue, 16 Jun 2020 08:09:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:22: #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 08:09:23: #1 tags after filtering in treatment: 19723492 INFO @ Tue, 16 Jun 2020 08:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:24: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 08:09:24: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:24: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:09:24: #2 alternative fragment length(s) may be 1,47 bps INFO @ Tue, 16 Jun 2020 08:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:24: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Tue, 16 Jun 2020 08:09:24: #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 08:09:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:24: 15000000 INFO @ Tue, 16 Jun 2020 08:09:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:30: 16000000 INFO @ Tue, 16 Jun 2020 08:09:36: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:43: 18000000 INFO @ Tue, 16 Jun 2020 08:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (626 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:49: 19000000 INFO @ Tue, 16 Jun 2020 08:09:54: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:09:54: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:09:54: #1 total tags in treatment: 19723492 INFO @ Tue, 16 Jun 2020 08:09:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:54: #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 08:09:54: #1 tags after filtering in treatment: 19723492 INFO @ Tue, 16 Jun 2020 08:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:55: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 08:09:55: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:55: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:09:55: #2 alternative fragment length(s) may be 1,47 bps INFO @ Tue, 16 Jun 2020 08:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:55: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Tue, 16 Jun 2020 08:09:55: #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 08:09:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:10:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936239/SRX1936239.20_summits.bed INFO @ Tue, 16 Jun 2020 08:10:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling