Job ID = 6366835 SRX = SRX2350734 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:08:08 prefetch.2.10.7: 1) Downloading 'SRR5024043'... 2020-06-15T23:08:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:10:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:10:19 prefetch.2.10.7: 'SRR5024043' is valid 2020-06-15T23:10:19 prefetch.2.10.7: 1) 'SRR5024043' was downloaded successfully Read 11177939 spots for SRR5024043/SRR5024043.sra Written 11177939 spots for SRR5024043/SRR5024043.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: 00:02:55 11177939 reads; of these: 11177939 (100.00%) were unpaired; of these: 315222 (2.82%) aligned 0 times 8704895 (77.88%) aligned exactly 1 time 2157822 (19.30%) aligned >1 times 97.18% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 1280418 / 10862717 = 0.1179 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 08:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.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 08:16:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:07: 1000000 INFO @ Tue, 16 Jun 2020 08:17:14: 2000000 INFO @ Tue, 16 Jun 2020 08:17:21: 3000000 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 08:17:28: 4000000 INFO @ Tue, 16 Jun 2020 08:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.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 08:17:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:36: 5000000 INFO @ Tue, 16 Jun 2020 08:17:37: 1000000 INFO @ Tue, 16 Jun 2020 08:17:44: 2000000 INFO @ Tue, 16 Jun 2020 08:17:45: 6000000 INFO @ Tue, 16 Jun 2020 08:17:52: 3000000 INFO @ Tue, 16 Jun 2020 08:17:53: 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 08:17:59: 4000000 INFO @ Tue, 16 Jun 2020 08:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.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 08:17:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:01: 8000000 INFO @ Tue, 16 Jun 2020 08:18:07: 1000000 INFO @ Tue, 16 Jun 2020 08:18:07: 5000000 INFO @ Tue, 16 Jun 2020 08:18:09: 9000000 INFO @ Tue, 16 Jun 2020 08:18:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:14: #1 total tags in treatment: 9582299 INFO @ Tue, 16 Jun 2020 08:18:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:14: #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 08:18:14: #1 tags after filtering in treatment: 9582299 INFO @ Tue, 16 Jun 2020 08:18:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:14: 2000000 INFO @ Tue, 16 Jun 2020 08:18:15: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 08:18:15: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:15: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:18:15: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.05_model.r WARNING @ Tue, 16 Jun 2020 08:18:15: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:15: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:18:15: #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 08:18:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:15: 6000000 INFO @ Tue, 16 Jun 2020 08:18:21: 3000000 INFO @ Tue, 16 Jun 2020 08:18:22: 7000000 INFO @ Tue, 16 Jun 2020 08:18:28: 4000000 INFO @ Tue, 16 Jun 2020 08:18:29: 8000000 INFO @ Tue, 16 Jun 2020 08:18:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:35: 5000000 INFO @ Tue, 16 Jun 2020 08:18:36: 9000000 INFO @ Tue, 16 Jun 2020 08:18:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:40: #1 total tags in treatment: 9582299 INFO @ Tue, 16 Jun 2020 08:18:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:40: #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 08:18:41: #1 tags after filtering in treatment: 9582299 INFO @ Tue, 16 Jun 2020 08:18:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:41: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 08:18:41: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:41: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:18:41: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:18:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:41: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:18:41: #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 08:18:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:42: 6000000 INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (680 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:48: 7000000 INFO @ Tue, 16 Jun 2020 08:18:55: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:01: 9000000 INFO @ Tue, 16 Jun 2020 08:19:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:05: #1 total tags in treatment: 9582299 INFO @ Tue, 16 Jun 2020 08:19:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:05: #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 08:19:05: #1 tags after filtering in treatment: 9582299 INFO @ Tue, 16 Jun 2020 08:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:06: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 08:19:06: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:06: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:19:06: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.20_model.r WARNING @ Tue, 16 Jun 2020 08:19:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:06: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:19:06: #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 08:19:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (386 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350734/SRX2350734.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling