Job ID = 6366858 SRX = SRX235166 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 'SRR708613'... 2020-06-15T23:06:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:29 prefetch.2.10.7: 'SRR708613' is valid 2020-06-15T23:06:29 prefetch.2.10.7: 1) 'SRR708613' was downloaded successfully Read 4160867 spots for SRR708613/SRR708613.sra Written 4160867 spots for SRR708613/SRR708613.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: 00:00:41 4160867 reads; of these: 4160867 (100.00%) were unpaired; of these: 208890 (5.02%) aligned 0 times 3298835 (79.28%) aligned exactly 1 time 653142 (15.70%) aligned >1 times 94.98% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 1064734 / 3951977 = 0.2694 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 08:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.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 08:08:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:36: 1000000 INFO @ Tue, 16 Jun 2020 08:08:41: 2000000 INFO @ Tue, 16 Jun 2020 08:08:45: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:45: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:45: #1 total tags in treatment: 2887243 INFO @ Tue, 16 Jun 2020 08:08:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:45: #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 08:08:45: #1 tags after filtering in treatment: 2887243 INFO @ Tue, 16 Jun 2020 08:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:45: #2 number of paired peaks: 285 WARNING @ Tue, 16 Jun 2020 08:08:45: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:45: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:08:45: #2 alternative fragment length(s) may be 16,42,75,102,139,210,236,280,340,407,510,547,576 bps INFO @ Tue, 16 Jun 2020 08:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:45: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:45: #2 You may need to consider one of the other alternative d(s): 16,42,75,102,139,210,236,280,340,407,510,547,576 WARNING @ Tue, 16 Jun 2020 08:08:45: #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 08:08:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.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 08:09:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:07: 1000000 INFO @ Tue, 16 Jun 2020 08:09:12: 2000000 INFO @ Tue, 16 Jun 2020 08:09:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:17: #1 total tags in treatment: 2887243 INFO @ Tue, 16 Jun 2020 08:09:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:17: #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 08:09:17: #1 tags after filtering in treatment: 2887243 INFO @ Tue, 16 Jun 2020 08:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:17: #2 number of paired peaks: 285 WARNING @ Tue, 16 Jun 2020 08:09:17: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:17: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:09:17: #2 alternative fragment length(s) may be 16,42,75,102,139,210,236,280,340,407,510,547,576 bps INFO @ Tue, 16 Jun 2020 08:09:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:17: #2 You may need to consider one of the other alternative d(s): 16,42,75,102,139,210,236,280,340,407,510,547,576 WARNING @ Tue, 16 Jun 2020 08:09:17: #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 08:09:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (55 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.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 08:09:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:36: 1000000 INFO @ Tue, 16 Jun 2020 08:09:41: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:46: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:09:46: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:09:46: #1 total tags in treatment: 2887243 INFO @ Tue, 16 Jun 2020 08:09:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:46: #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 08:09:46: #1 tags after filtering in treatment: 2887243 INFO @ Tue, 16 Jun 2020 08:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:46: #2 number of paired peaks: 285 WARNING @ Tue, 16 Jun 2020 08:09:46: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:46: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:09:46: #2 alternative fragment length(s) may be 16,42,75,102,139,210,236,280,340,407,510,547,576 bps INFO @ Tue, 16 Jun 2020 08:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:46: #2 You may need to consider one of the other alternative d(s): 16,42,75,102,139,210,236,280,340,407,510,547,576 WARNING @ Tue, 16 Jun 2020 08:09:46: #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 08:09:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX235166/SRX235166.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling