Job ID = 6367696 SRX = SRX3942559 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:05 prefetch.2.10.7: 1) Downloading 'SRR7010080'... 2020-06-15T23:35:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:09 prefetch.2.10.7: 'SRR7010080' is valid 2020-06-15T23:38:09 prefetch.2.10.7: 1) 'SRR7010080' was downloaded successfully 2020-06-15T23:38:09 prefetch.2.10.7: 'SRR7010080' has 0 unresolved dependencies Read 17101099 spots for SRR7010080/SRR7010080.sra Written 17101099 spots for SRR7010080/SRR7010080.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: 00:05:54 17101099 reads; of these: 17101099 (100.00%) were unpaired; of these: 1669089 (9.76%) aligned 0 times 12934744 (75.64%) aligned exactly 1 time 2497266 (14.60%) aligned >1 times 90.24% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 3256586 / 15432010 = 0.2110 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 08:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.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 08:49:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:16: 1000000 INFO @ Tue, 16 Jun 2020 08:49:22: 2000000 INFO @ Tue, 16 Jun 2020 08:49:29: 3000000 INFO @ Tue, 16 Jun 2020 08:49:35: 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 08:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.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 08:49:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:43: 5000000 INFO @ Tue, 16 Jun 2020 08:49:49: 1000000 INFO @ Tue, 16 Jun 2020 08:49:51: 6000000 INFO @ Tue, 16 Jun 2020 08:49:58: 2000000 INFO @ Tue, 16 Jun 2020 08:49:59: 7000000 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 08:50:08: 3000000 INFO @ Tue, 16 Jun 2020 08:50:08: 8000000 INFO @ Tue, 16 Jun 2020 08:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.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 08:50:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:16: 9000000 INFO @ Tue, 16 Jun 2020 08:50:17: 4000000 INFO @ Tue, 16 Jun 2020 08:50:18: 1000000 INFO @ Tue, 16 Jun 2020 08:50:24: 10000000 INFO @ Tue, 16 Jun 2020 08:50:26: 2000000 INFO @ Tue, 16 Jun 2020 08:50:26: 5000000 INFO @ Tue, 16 Jun 2020 08:50:32: 11000000 INFO @ Tue, 16 Jun 2020 08:50:34: 3000000 INFO @ Tue, 16 Jun 2020 08:50:36: 6000000 INFO @ Tue, 16 Jun 2020 08:50:41: 12000000 INFO @ Tue, 16 Jun 2020 08:50:42: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:50:42: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:50:42: #1 total tags in treatment: 12175424 INFO @ Tue, 16 Jun 2020 08:50:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:42: #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 08:50:42: #1 tags after filtering in treatment: 12175424 INFO @ Tue, 16 Jun 2020 08:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:42: 4000000 INFO @ Tue, 16 Jun 2020 08:50:43: #2 number of paired peaks: 298 WARNING @ Tue, 16 Jun 2020 08:50:43: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:43: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:50:43: #2 alternative fragment length(s) may be 3,64,575 bps INFO @ Tue, 16 Jun 2020 08:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:43: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:43: #2 You may need to consider one of the other alternative d(s): 3,64,575 WARNING @ Tue, 16 Jun 2020 08:50:43: #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 08:50:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:45: 7000000 INFO @ Tue, 16 Jun 2020 08:50:50: 5000000 INFO @ Tue, 16 Jun 2020 08:50:54: 8000000 INFO @ Tue, 16 Jun 2020 08:50:59: 6000000 INFO @ Tue, 16 Jun 2020 08:51:04: 9000000 INFO @ Tue, 16 Jun 2020 08:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:07: 7000000 INFO @ Tue, 16 Jun 2020 08:51:13: 10000000 INFO @ Tue, 16 Jun 2020 08:51:15: 8000000 INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:22: 11000000 INFO @ Tue, 16 Jun 2020 08:51:23: 9000000 INFO @ Tue, 16 Jun 2020 08:51:30: 12000000 INFO @ Tue, 16 Jun 2020 08:51:31: 10000000 INFO @ Tue, 16 Jun 2020 08:51:32: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:51:32: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:51:32: #1 total tags in treatment: 12175424 INFO @ Tue, 16 Jun 2020 08:51:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:32: #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 08:51:32: #1 tags after filtering in treatment: 12175424 INFO @ Tue, 16 Jun 2020 08:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:33: #2 number of paired peaks: 298 WARNING @ Tue, 16 Jun 2020 08:51:33: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:33: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:51:33: #2 alternative fragment length(s) may be 3,64,575 bps INFO @ Tue, 16 Jun 2020 08:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.10_model.r WARNING @ Tue, 16 Jun 2020 08:51:33: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:33: #2 You may need to consider one of the other alternative d(s): 3,64,575 WARNING @ Tue, 16 Jun 2020 08:51:33: #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 08:51:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:38: 11000000 INFO @ Tue, 16 Jun 2020 08:51:45: 12000000 INFO @ Tue, 16 Jun 2020 08:51:46: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:51:46: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:51:46: #1 total tags in treatment: 12175424 INFO @ Tue, 16 Jun 2020 08:51:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:46: #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 08:51:46: #1 tags after filtering in treatment: 12175424 INFO @ Tue, 16 Jun 2020 08:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:46: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:47: #2 number of paired peaks: 298 WARNING @ Tue, 16 Jun 2020 08:51:47: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:47: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:51:47: #2 alternative fragment length(s) may be 3,64,575 bps INFO @ Tue, 16 Jun 2020 08:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:47: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:47: #2 You may need to consider one of the other alternative d(s): 3,64,575 WARNING @ Tue, 16 Jun 2020 08:51:47: #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 08:51:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.10_summits.bed INFO @ Tue, 16 Jun 2020 08:52:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942559/SRX3942559.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling