Job ID = 6453225 SRX = SRX109550 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:10:04 prefetch.2.10.7: 1) Downloading 'SRR385747'... 2020-06-21T08:10:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:11:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:11:36 prefetch.2.10.7: 'SRR385747' is valid 2020-06-21T08:11:36 prefetch.2.10.7: 1) 'SRR385747' was downloaded successfully Read 7077117 spots for SRR385747/SRR385747.sra Written 7077117 spots for SRR385747/SRR385747.sra 2020-06-21T08:12:05 prefetch.2.10.7: 1) Downloading 'SRR385748'... 2020-06-21T08:12:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:12:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:12:29 prefetch.2.10.7: 'SRR385748' is valid 2020-06-21T08:12:29 prefetch.2.10.7: 1) 'SRR385748' was downloaded successfully Read 2770491 spots for SRR385748/SRR385748.sra Written 2770491 spots for SRR385748/SRR385748.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: 00:00:56 9847608 reads; of these: 9847608 (100.00%) were unpaired; of these: 7326577 (74.40%) aligned 0 times 2079812 (21.12%) aligned exactly 1 time 441219 (4.48%) aligned >1 times 25.60% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 213862 / 2521031 = 0.0848 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 @ Sun, 21 Jun 2020 17:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:14:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:46: 1000000 INFO @ Sun, 21 Jun 2020 17:14:52: 2000000 INFO @ Sun, 21 Jun 2020 17:14:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:14:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:14:54: #1 total tags in treatment: 2307169 INFO @ Sun, 21 Jun 2020 17:14:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:14:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:14:54: #1 tags after filtering in treatment: 2306930 INFO @ Sun, 21 Jun 2020 17:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:14:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:14:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:14:54: #2 number of paired peaks: 675 WARNING @ Sun, 21 Jun 2020 17:14:54: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Sun, 21 Jun 2020 17:14:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:14:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:14:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:14:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:14:54: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 17:14:54: #2 alternative fragment length(s) may be 71,570 bps INFO @ Sun, 21 Jun 2020 17:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.05_model.r WARNING @ Sun, 21 Jun 2020 17:14:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:14:54: #2 You may need to consider one of the other alternative d(s): 71,570 WARNING @ Sun, 21 Jun 2020 17:14:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:14:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.05_summits.bed INFO @ Sun, 21 Jun 2020 17:15:03: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 5 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 @ Sun, 21 Jun 2020 17:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:15:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:16: 1000000 INFO @ Sun, 21 Jun 2020 17:15:22: 2000000 INFO @ Sun, 21 Jun 2020 17:15:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:23: #1 total tags in treatment: 2307169 INFO @ Sun, 21 Jun 2020 17:15:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:15:24: #1 tags after filtering in treatment: 2306930 INFO @ Sun, 21 Jun 2020 17:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:24: #2 number of paired peaks: 675 WARNING @ Sun, 21 Jun 2020 17:15:24: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Sun, 21 Jun 2020 17:15:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:24: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 17:15:24: #2 alternative fragment length(s) may be 71,570 bps INFO @ Sun, 21 Jun 2020 17:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.10_model.r WARNING @ Sun, 21 Jun 2020 17:15:24: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:15:24: #2 You may need to consider one of the other alternative d(s): 71,570 WARNING @ Sun, 21 Jun 2020 17:15:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:15:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:15:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:15:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.10_summits.bed INFO @ Sun, 21 Jun 2020 17:15:32: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 3 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 @ Sun, 21 Jun 2020 17:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:15:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:46: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:15:52: 2000000 INFO @ Sun, 21 Jun 2020 17:15:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:54: #1 total tags in treatment: 2307169 INFO @ Sun, 21 Jun 2020 17:15:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:15:54: #1 tags after filtering in treatment: 2306930 INFO @ Sun, 21 Jun 2020 17:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:54: #2 number of paired peaks: 675 WARNING @ Sun, 21 Jun 2020 17:15:54: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Sun, 21 Jun 2020 17:15:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:54: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 17:15:54: #2 alternative fragment length(s) may be 71,570 bps INFO @ Sun, 21 Jun 2020 17:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.20_model.r WARNING @ Sun, 21 Jun 2020 17:15:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:15:54: #2 You may need to consider one of the other alternative d(s): 71,570 WARNING @ Sun, 21 Jun 2020 17:15:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:15:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:16:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX109550/SRX109550.20_summits.bed INFO @ Sun, 21 Jun 2020 17:16:03: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling