Job ID = 6366900 SRX = SRX257645 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:13 prefetch.2.10.7: 1) Downloading 'SRR800656'... 2020-06-15T23:02:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:15 prefetch.2.10.7: 1) 'SRR800656' was downloaded successfully Read 16172133 spots for SRR800656/SRR800656.sra Written 16172133 spots for SRR800656/SRR800656.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: 00:03:48 16172133 reads; of these: 16172133 (100.00%) were unpaired; of these: 283363 (1.75%) aligned 0 times 13078679 (80.87%) aligned exactly 1 time 2810091 (17.38%) aligned >1 times 98.25% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 5750765 / 15888770 = 0.3619 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 08:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.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 08:12:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:19: 1000000 INFO @ Tue, 16 Jun 2020 08:12:27: 2000000 INFO @ Tue, 16 Jun 2020 08:12:35: 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 08:12:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.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 08:12:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:43: 4000000 INFO @ Tue, 16 Jun 2020 08:12:49: 1000000 INFO @ Tue, 16 Jun 2020 08:12:52: 5000000 INFO @ Tue, 16 Jun 2020 08:12:57: 2000000 INFO @ Tue, 16 Jun 2020 08:13:00: 6000000 INFO @ Tue, 16 Jun 2020 08:13:04: 3000000 INFO @ Tue, 16 Jun 2020 08:13:08: 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 08:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.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 08:13:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:12: 4000000 INFO @ Tue, 16 Jun 2020 08:13:16: 8000000 INFO @ Tue, 16 Jun 2020 08:13:19: 1000000 INFO @ Tue, 16 Jun 2020 08:13:20: 5000000 INFO @ Tue, 16 Jun 2020 08:13:25: 9000000 INFO @ Tue, 16 Jun 2020 08:13:27: 2000000 INFO @ Tue, 16 Jun 2020 08:13:27: 6000000 INFO @ Tue, 16 Jun 2020 08:13:33: 10000000 INFO @ Tue, 16 Jun 2020 08:13:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:34: #1 total tags in treatment: 10138005 INFO @ Tue, 16 Jun 2020 08:13:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:34: #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 08:13:34: #1 tags after filtering in treatment: 10138005 INFO @ Tue, 16 Jun 2020 08:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:34: 3000000 INFO @ Tue, 16 Jun 2020 08:13:35: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 08:13:35: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:35: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:13:35: #2 alternative fragment length(s) may be 2,51,556,577 bps INFO @ Tue, 16 Jun 2020 08:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.05_model.r WARNING @ Tue, 16 Jun 2020 08:13:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:35: #2 You may need to consider one of the other alternative d(s): 2,51,556,577 WARNING @ Tue, 16 Jun 2020 08:13:35: #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 08:13:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:35: 7000000 INFO @ Tue, 16 Jun 2020 08:13:41: 4000000 INFO @ Tue, 16 Jun 2020 08:13:42: 8000000 INFO @ Tue, 16 Jun 2020 08:13:49: 5000000 INFO @ Tue, 16 Jun 2020 08:13:49: 9000000 INFO @ Tue, 16 Jun 2020 08:13:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:56: 6000000 INFO @ Tue, 16 Jun 2020 08:13:57: 10000000 INFO @ Tue, 16 Jun 2020 08:13:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:58: #1 total tags in treatment: 10138005 INFO @ Tue, 16 Jun 2020 08:13:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:58: #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 08:13:58: #1 tags after filtering in treatment: 10138005 INFO @ Tue, 16 Jun 2020 08:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:58: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 08:13:58: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:59: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:13:59: #2 alternative fragment length(s) may be 2,51,556,577 bps INFO @ Tue, 16 Jun 2020 08:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.10_model.r WARNING @ Tue, 16 Jun 2020 08:13:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:13:59: #2 You may need to consider one of the other alternative d(s): 2,51,556,577 WARNING @ Tue, 16 Jun 2020 08:13:59: #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 08:13:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:03: 7000000 INFO @ Tue, 16 Jun 2020 08:14:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (860 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:09: 8000000 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:15: 9000000 INFO @ Tue, 16 Jun 2020 08:14:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:21: 10000000 INFO @ Tue, 16 Jun 2020 08:14:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:22: #1 total tags in treatment: 10138005 INFO @ Tue, 16 Jun 2020 08:14:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:22: #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 08:14:22: #1 tags after filtering in treatment: 10138005 INFO @ Tue, 16 Jun 2020 08:14:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:23: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 08:14:23: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:23: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:14:23: #2 alternative fragment length(s) may be 2,51,556,577 bps INFO @ Tue, 16 Jun 2020 08:14:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.20_model.r WARNING @ Tue, 16 Jun 2020 08:14:23: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:23: #2 You may need to consider one of the other alternative d(s): 2,51,556,577 WARNING @ Tue, 16 Jun 2020 08:14:23: #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 08:14:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (558 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257645/SRX257645.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling