Job ID = 6366729 SRX = SRX2228882 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:08 prefetch.2.10.7: 1) Downloading 'SRR4380338'... 2020-06-15T23:07:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:47 prefetch.2.10.7: 'SRR4380338' is valid 2020-06-15T23:08:47 prefetch.2.10.7: 1) 'SRR4380338' was downloaded successfully 2020-06-15T23:08:47 prefetch.2.10.7: 'SRR4380338' has 0 unresolved dependencies Read 20627992 spots for SRR4380338/SRR4380338.sra Written 20627992 spots for SRR4380338/SRR4380338.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: 00:02:17 20627992 reads; of these: 20627992 (100.00%) were unpaired; of these: 16616964 (80.56%) aligned 0 times 3252051 (15.77%) aligned exactly 1 time 758977 (3.68%) aligned >1 times 19.44% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 547260 / 4011028 = 0.1364 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 08:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.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 08:13:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:57: 1000000 INFO @ Tue, 16 Jun 2020 08:14:03: 2000000 INFO @ Tue, 16 Jun 2020 08:14:10: 3000000 INFO @ Tue, 16 Jun 2020 08:14:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:13: #1 total tags in treatment: 3463768 INFO @ Tue, 16 Jun 2020 08:14:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:13: #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 08:14:13: #1 tags after filtering in treatment: 3463768 INFO @ Tue, 16 Jun 2020 08:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:13: #2 number of paired peaks: 455 WARNING @ Tue, 16 Jun 2020 08:14:13: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:13: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:14:13: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:13: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:13: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:14:13: #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 08:14:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:13: #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 08:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.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 08:14:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:26: Done! INFO @ Tue, 16 Jun 2020 08:14:26: 1000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (572 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:31: 2000000 INFO @ Tue, 16 Jun 2020 08:14:37: 3000000 INFO @ Tue, 16 Jun 2020 08:14:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:39: #1 total tags in treatment: 3463768 INFO @ Tue, 16 Jun 2020 08:14:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:39: #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 08:14:39: #1 tags after filtering in treatment: 3463768 INFO @ Tue, 16 Jun 2020 08:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:40: #2 number of paired peaks: 455 WARNING @ Tue, 16 Jun 2020 08:14:40: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:40: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:14:40: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.10_model.r WARNING @ Tue, 16 Jun 2020 08:14:40: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:40: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:14:40: #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 08:14:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:48: #3 Call peaks for each chromosome... 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 08:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.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 08:14:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:57: 1000000 INFO @ Tue, 16 Jun 2020 08:15:03: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:09: 3000000 INFO @ Tue, 16 Jun 2020 08:15:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:12: #1 total tags in treatment: 3463768 INFO @ Tue, 16 Jun 2020 08:15:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:12: #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 08:15:12: #1 tags after filtering in treatment: 3463768 INFO @ Tue, 16 Jun 2020 08:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:13: #2 number of paired peaks: 455 WARNING @ Tue, 16 Jun 2020 08:15:13: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:13: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:15:13: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:13: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:13: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:15:13: #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 08:15:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228882/SRX2228882.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling