Job ID = 6365926 SRX = SRX043859 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:23:44 prefetch.2.10.7: 1) Downloading 'SRR107317'... 2020-06-15T22:23:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:24:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:24:24 prefetch.2.10.7: 'SRR107317' is valid 2020-06-15T22:24:24 prefetch.2.10.7: 1) 'SRR107317' was downloaded successfully Read 5909704 spots for SRR107317/SRR107317.sra Written 5909704 spots for SRR107317/SRR107317.sra 2020-06-15T22:24:52 prefetch.2.10.7: 1) Downloading 'SRR107318'... 2020-06-15T22:24:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:25:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:25:16 prefetch.2.10.7: 'SRR107318' is valid 2020-06-15T22:25:16 prefetch.2.10.7: 1) 'SRR107318' was downloaded successfully Read 2601048 spots for SRR107318/SRR107318.sra Written 2601048 spots for SRR107318/SRR107318.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:41 8510752 reads; of these: 8510752 (100.00%) were unpaired; of these: 7462598 (87.68%) aligned 0 times 919445 (10.80%) aligned exactly 1 time 128709 (1.51%) aligned >1 times 12.32% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 33373 / 1048154 = 0.0318 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 07:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.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 07:26:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:04: 1000000 INFO @ Tue, 16 Jun 2020 07:27:04: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:27:04: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:27:04: #1 total tags in treatment: 1014781 INFO @ Tue, 16 Jun 2020 07:27:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:04: #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 07:27:04: #1 tags after filtering in treatment: 1014781 INFO @ Tue, 16 Jun 2020 07:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:05: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 07:27:05: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:05: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 07:27:05: #2 alternative fragment length(s) may be 40,48,113,204,288,460,479,500,594 bps INFO @ Tue, 16 Jun 2020 07:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.05_model.r WARNING @ Tue, 16 Jun 2020 07:27:05: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:27:05: #2 You may need to consider one of the other alternative d(s): 40,48,113,204,288,460,479,500,594 WARNING @ Tue, 16 Jun 2020 07:27:05: #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 07:27:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:27:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.05_summits.bed INFO @ Tue, 16 Jun 2020 07:27:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 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 07:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.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 07:27:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:27:35: 1000000 INFO @ Tue, 16 Jun 2020 07:27:35: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:27:35: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:27:35: #1 total tags in treatment: 1014781 INFO @ Tue, 16 Jun 2020 07:27:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:35: #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 07:27:35: #1 tags after filtering in treatment: 1014781 INFO @ Tue, 16 Jun 2020 07:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:35: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:35: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 07:27:35: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:35: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 07:27:35: #2 alternative fragment length(s) may be 40,48,113,204,288,460,479,500,594 bps INFO @ Tue, 16 Jun 2020 07:27:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.10_model.r WARNING @ Tue, 16 Jun 2020 07:27:35: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:27:35: #2 You may need to consider one of the other alternative d(s): 40,48,113,204,288,460,479,500,594 WARNING @ Tue, 16 Jun 2020 07:27:35: #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 07:27:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:27:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.10_summits.bed INFO @ Tue, 16 Jun 2020 07:27:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (15 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 07:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.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 07:27:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:27:59: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:28:04: 1000000 INFO @ Tue, 16 Jun 2020 07:28:05: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:28:05: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:28:05: #1 total tags in treatment: 1014781 INFO @ Tue, 16 Jun 2020 07:28:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:05: #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 07:28:05: #1 tags after filtering in treatment: 1014781 INFO @ Tue, 16 Jun 2020 07:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:05: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 07:28:05: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 07:28:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:05: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 07:28:05: #2 alternative fragment length(s) may be 40,48,113,204,288,460,479,500,594 bps INFO @ Tue, 16 Jun 2020 07:28:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.20_model.r WARNING @ Tue, 16 Jun 2020 07:28:05: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:28:05: #2 You may need to consider one of the other alternative d(s): 40,48,113,204,288,460,479,500,594 WARNING @ Tue, 16 Jun 2020 07:28:05: #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 07:28:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:28:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043859/SRX043859.20_summits.bed INFO @ Tue, 16 Jun 2020 07:28:08: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling