Job ID = 6366969 SRX = SRX257668 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:19:16 prefetch.2.10.7: 1) Downloading 'SRR800679'... 2020-06-15T23:19:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:08 prefetch.2.10.7: 1) 'SRR800679' was downloaded successfully Read 20216847 spots for SRR800679/SRR800679.sra Written 20216847 spots for SRR800679/SRR800679.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: 00:04:32 20216847 reads; of these: 20216847 (100.00%) were unpaired; of these: 1061184 (5.25%) aligned 0 times 15881887 (78.56%) aligned exactly 1 time 3273776 (16.19%) aligned >1 times 94.75% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 15365640 / 19155663 = 0.8021 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 08:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.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 08:31:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:31: 1000000 INFO @ Tue, 16 Jun 2020 08:31:37: 2000000 INFO @ Tue, 16 Jun 2020 08:31:43: 3000000 INFO @ Tue, 16 Jun 2020 08:31:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:31:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:31:47: #1 total tags in treatment: 3790023 INFO @ Tue, 16 Jun 2020 08:31:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:47: #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 08:31:47: #1 tags after filtering in treatment: 3790023 INFO @ Tue, 16 Jun 2020 08:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:48: #2 number of paired peaks: 976 WARNING @ Tue, 16 Jun 2020 08:31:48: Fewer paired peaks (976) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 976 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:48: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 08:31:48: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 08:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:48: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:48: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 16 Jun 2020 08:31:48: #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 08:31:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:48: #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 08:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.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 08:31:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1252 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:02: 1000000 INFO @ Tue, 16 Jun 2020 08:32:09: 2000000 INFO @ Tue, 16 Jun 2020 08:32:16: 3000000 INFO @ Tue, 16 Jun 2020 08:32:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:22: #1 total tags in treatment: 3790023 INFO @ Tue, 16 Jun 2020 08:32:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:22: #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 08:32:22: #1 tags after filtering in treatment: 3790023 INFO @ Tue, 16 Jun 2020 08:32:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:22: #2 number of paired peaks: 976 WARNING @ Tue, 16 Jun 2020 08:32:22: Fewer paired peaks (976) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 976 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:22: start model_add_line... BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:32:22: start X-correlation... 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 08:32:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:22: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 08:32:22: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 08:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:22: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:22: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 16 Jun 2020 08:32:22: #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 08:32:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.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 08:32:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:31: 1000000 INFO @ Tue, 16 Jun 2020 08:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (719 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:38: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:45: 3000000 INFO @ Tue, 16 Jun 2020 08:32:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:50: #1 total tags in treatment: 3790023 INFO @ Tue, 16 Jun 2020 08:32:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:50: #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 08:32:50: #1 tags after filtering in treatment: 3790023 INFO @ Tue, 16 Jun 2020 08:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:51: #2 number of paired peaks: 976 WARNING @ Tue, 16 Jun 2020 08:32:51: Fewer paired peaks (976) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 976 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:51: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 08:32:51: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 08:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.20_model.r WARNING @ Tue, 16 Jun 2020 08:32:51: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:51: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 16 Jun 2020 08:32:51: #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 08:32:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257668/SRX257668.20_summits.bed INFO @ Tue, 16 Jun 2020 08:33:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 2 millis CompletedMACS2peakCalling