Job ID = 6366901 SRX = SRX257646 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:08 prefetch.2.10.7: 1) Downloading 'SRR800657'... 2020-06-15T23:06:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:55 prefetch.2.10.7: 1) 'SRR800657' was downloaded successfully Read 18091038 spots for SRR800657/SRR800657.sra Written 18091038 spots for SRR800657/SRR800657.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: 00:03:57 18091038 reads; of these: 18091038 (100.00%) were unpaired; of these: 454852 (2.51%) aligned 0 times 14719787 (81.37%) aligned exactly 1 time 2916399 (16.12%) aligned >1 times 97.49% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 11532837 / 17636186 = 0.6539 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 08:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.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 08:17:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:44: 1000000 INFO @ Tue, 16 Jun 2020 08:17:51: 2000000 INFO @ Tue, 16 Jun 2020 08:17:57: 3000000 INFO @ Tue, 16 Jun 2020 08:18:04: 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 08:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.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 08:18:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:11: 5000000 INFO @ Tue, 16 Jun 2020 08:18:15: 1000000 INFO @ Tue, 16 Jun 2020 08:18:18: 6000000 INFO @ Tue, 16 Jun 2020 08:18:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:18: #1 total tags in treatment: 6103349 INFO @ Tue, 16 Jun 2020 08:18:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:18: #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 08:18:18: #1 tags after filtering in treatment: 6103349 INFO @ Tue, 16 Jun 2020 08:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:19: #2 number of paired peaks: 657 WARNING @ Tue, 16 Jun 2020 08:18:19: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:19: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 08:18:19: #2 alternative fragment length(s) may be 4,54,540,567 bps INFO @ Tue, 16 Jun 2020 08:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.05_model.r WARNING @ Tue, 16 Jun 2020 08:18:19: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:19: #2 You may need to consider one of the other alternative d(s): 4,54,540,567 WARNING @ Tue, 16 Jun 2020 08:18:19: #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 08:18:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:22: 2000000 INFO @ Tue, 16 Jun 2020 08:18:28: 3000000 INFO @ Tue, 16 Jun 2020 08:18:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:35: 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 08:18:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.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 08:18:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:41: 5000000 INFO @ Tue, 16 Jun 2020 08:18:46: 1000000 INFO @ Tue, 16 Jun 2020 08:18:48: 6000000 INFO @ Tue, 16 Jun 2020 08:18:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:49: #1 total tags in treatment: 6103349 INFO @ Tue, 16 Jun 2020 08:18:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:49: #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 08:18:49: #1 tags after filtering in treatment: 6103349 INFO @ Tue, 16 Jun 2020 08:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:50: #2 number of paired peaks: 657 WARNING @ Tue, 16 Jun 2020 08:18:50: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:50: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 08:18:50: #2 alternative fragment length(s) may be 4,54,540,567 bps INFO @ Tue, 16 Jun 2020 08:18:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:50: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:50: #2 You may need to consider one of the other alternative d(s): 4,54,540,567 WARNING @ Tue, 16 Jun 2020 08:18:50: #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 08:18:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:53: 2000000 INFO @ Tue, 16 Jun 2020 08:18:59: 3000000 INFO @ Tue, 16 Jun 2020 08:19:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:06: 4000000 INFO @ Tue, 16 Jun 2020 08:19:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (618 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:12: 5000000 INFO @ Tue, 16 Jun 2020 08:19:19: 6000000 INFO @ Tue, 16 Jun 2020 08:19:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:20: #1 total tags in treatment: 6103349 INFO @ Tue, 16 Jun 2020 08:19:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:20: #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 08:19:20: #1 tags after filtering in treatment: 6103349 INFO @ Tue, 16 Jun 2020 08:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:20: #2 number of paired peaks: 657 WARNING @ Tue, 16 Jun 2020 08:19:20: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:20: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 08:19:20: #2 alternative fragment length(s) may be 4,54,540,567 bps INFO @ Tue, 16 Jun 2020 08:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.20_model.r WARNING @ Tue, 16 Jun 2020 08:19:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:20: #2 You may need to consider one of the other alternative d(s): 4,54,540,567 WARNING @ Tue, 16 Jun 2020 08:19:20: #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 08:19:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257646/SRX257646.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (272 records, 4 fields): 2 millis CompletedMACS2peakCalling