Job ID = 6367145 SRX = SRX277103 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:39:44 prefetch.2.10.7: 1) Downloading 'SRR849779'... 2020-06-15T23:39:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:45 prefetch.2.10.7: 'SRR849779' is valid 2020-06-15T23:40:45 prefetch.2.10.7: 1) 'SRR849779' was downloaded successfully Read 6887983 spots for SRR849779/SRR849779.sra Written 6887983 spots for SRR849779/SRR849779.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: 00:01:05 6887983 reads; of these: 6887983 (100.00%) were unpaired; of these: 1034704 (15.02%) aligned 0 times 4986835 (72.40%) aligned exactly 1 time 866444 (12.58%) aligned >1 times 84.98% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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_rmdupse_core] 639605 / 5853279 = 0.1093 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 08:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.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 08:43:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:49: 1000000 INFO @ Tue, 16 Jun 2020 08:43:54: 2000000 INFO @ Tue, 16 Jun 2020 08:43:59: 3000000 INFO @ Tue, 16 Jun 2020 08:44:04: 4000000 INFO @ Tue, 16 Jun 2020 08:44:10: 5000000 INFO @ Tue, 16 Jun 2020 08:44:11: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:44:11: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:44:11: #1 total tags in treatment: 5213674 INFO @ Tue, 16 Jun 2020 08:44:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:11: #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 08:44:11: #1 tags after filtering in treatment: 5213674 INFO @ Tue, 16 Jun 2020 08:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:11: #2 number of paired peaks: 401 WARNING @ Tue, 16 Jun 2020 08:44:11: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:11: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:44:11: #2 alternative fragment length(s) may be 3,31,525,545,566,592 bps INFO @ Tue, 16 Jun 2020 08:44:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.05_model.r WARNING @ Tue, 16 Jun 2020 08:44:11: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:11: #2 You may need to consider one of the other alternative d(s): 3,31,525,545,566,592 WARNING @ Tue, 16 Jun 2020 08:44:11: #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 08:44:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:11: #3 Pre-compute pvalue-qvalue table... 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 08:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.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 08:44:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:18: 1000000 INFO @ Tue, 16 Jun 2020 08:44:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:22: 2000000 INFO @ Tue, 16 Jun 2020 08:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:27: 3000000 INFO @ Tue, 16 Jun 2020 08:44:32: 4000000 INFO @ Tue, 16 Jun 2020 08:44:36: 5000000 INFO @ Tue, 16 Jun 2020 08:44:37: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:44:37: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:44:37: #1 total tags in treatment: 5213674 INFO @ Tue, 16 Jun 2020 08:44:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:37: #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 08:44:37: #1 tags after filtering in treatment: 5213674 INFO @ Tue, 16 Jun 2020 08:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:38: #2 number of paired peaks: 401 WARNING @ Tue, 16 Jun 2020 08:44:38: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:38: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:44:38: #2 alternative fragment length(s) may be 3,31,525,545,566,592 bps INFO @ Tue, 16 Jun 2020 08:44:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.10_model.r WARNING @ Tue, 16 Jun 2020 08:44:38: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:38: #2 You may need to consider one of the other alternative d(s): 3,31,525,545,566,592 WARNING @ Tue, 16 Jun 2020 08:44:38: #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 08:44:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:38: #3 Pre-compute pvalue-qvalue table... 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 08:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.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 08:44:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:48: 1000000 INFO @ Tue, 16 Jun 2020 08:44:53: 2000000 INFO @ Tue, 16 Jun 2020 08:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.10_summits.bed INFO @ Tue, 16 Jun 2020 08:44:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:58: 3000000 INFO @ Tue, 16 Jun 2020 08:45:02: 4000000 INFO @ Tue, 16 Jun 2020 08:45:07: 5000000 INFO @ Tue, 16 Jun 2020 08:45:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:45:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:45:08: #1 total tags in treatment: 5213674 INFO @ Tue, 16 Jun 2020 08:45:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:08: #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 08:45:08: #1 tags after filtering in treatment: 5213674 INFO @ Tue, 16 Jun 2020 08:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:09: #2 number of paired peaks: 401 WARNING @ Tue, 16 Jun 2020 08:45:09: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:09: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:45:09: #2 alternative fragment length(s) may be 3,31,525,545,566,592 bps INFO @ Tue, 16 Jun 2020 08:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.20_model.r WARNING @ Tue, 16 Jun 2020 08:45:09: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:09: #2 You may need to consider one of the other alternative d(s): 3,31,525,545,566,592 WARNING @ Tue, 16 Jun 2020 08:45:09: #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 08:45:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277103/SRX277103.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling