Job ID = 6457065 SRX = SRX4375829 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:34:55 prefetch.2.10.7: 1) Downloading 'SRR7506483'... 2020-06-21T11:34:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:07 prefetch.2.10.7: 'SRR7506483' is valid 2020-06-21T11:37:07 prefetch.2.10.7: 1) 'SRR7506483' was downloaded successfully Read 12528023 spots for SRR7506483/SRR7506483.sra Written 12528023 spots for SRR7506483/SRR7506483.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: 00:02:42 12528023 reads; of these: 12528023 (100.00%) were unpaired; of these: 4194487 (33.48%) aligned 0 times 6322743 (50.47%) aligned exactly 1 time 2010793 (16.05%) aligned >1 times 66.52% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1406125 / 8333536 = 0.1687 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 20:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.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 20:43:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:23: 1000000 INFO @ Sun, 21 Jun 2020 20:43:29: 2000000 INFO @ Sun, 21 Jun 2020 20:43:35: 3000000 INFO @ Sun, 21 Jun 2020 20:43:41: 4000000 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 20:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.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 20:43:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:48: 5000000 INFO @ Sun, 21 Jun 2020 20:43:55: 1000000 INFO @ Sun, 21 Jun 2020 20:43:55: 6000000 INFO @ Sun, 21 Jun 2020 20:44:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:02: #1 total tags in treatment: 6927411 INFO @ Sun, 21 Jun 2020 20:44:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:02: #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 20:44:02: #1 tags after filtering in treatment: 6927269 INFO @ Sun, 21 Jun 2020 20:44:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:03: 2000000 INFO @ Sun, 21 Jun 2020 20:44:03: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 20:44:03: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 20:44:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:03: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 20:44:03: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 21 Jun 2020 20:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.05_model.r WARNING @ Sun, 21 Jun 2020 20:44:03: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:44:03: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 21 Jun 2020 20:44:03: #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 20:44:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:10: 3000000 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 20:44:17: 4000000 INFO @ Sun, 21 Jun 2020 20:44:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.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 20:44:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:24: 1000000 INFO @ Sun, 21 Jun 2020 20:44:24: 5000000 INFO @ Sun, 21 Jun 2020 20:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.05_summits.bed INFO @ Sun, 21 Jun 2020 20:44:27: Done! pass1 - making usageList (628 chroms): 1 millis pass2 - checking and writing primary data (2642 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:31: 2000000 INFO @ Sun, 21 Jun 2020 20:44:32: 6000000 INFO @ Sun, 21 Jun 2020 20:44:38: 3000000 INFO @ Sun, 21 Jun 2020 20:44:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:39: #1 total tags in treatment: 6927411 INFO @ Sun, 21 Jun 2020 20:44:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:39: #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 20:44:40: #1 tags after filtering in treatment: 6927269 INFO @ Sun, 21 Jun 2020 20:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:40: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 20:44:40: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 20:44:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:40: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:40: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:40: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:40: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 20:44:40: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 21 Jun 2020 20:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.10_model.r WARNING @ Sun, 21 Jun 2020 20:44:40: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:44:40: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 21 Jun 2020 20:44:40: #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 20:44:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:45: 4000000 INFO @ Sun, 21 Jun 2020 20:44:51: 5000000 INFO @ Sun, 21 Jun 2020 20:44:55: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:57: 6000000 INFO @ Sun, 21 Jun 2020 20:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.10_summits.bed INFO @ Sun, 21 Jun 2020 20:45:03: Done! INFO @ Sun, 21 Jun 2020 20:45:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:45:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:45:03: #1 total tags in treatment: 6927411 INFO @ Sun, 21 Jun 2020 20:45:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (884 records, 4 fields): 11 millis INFO @ Sun, 21 Jun 2020 20:45:03: #1 tags after filtering in treatment: 6927269 INFO @ Sun, 21 Jun 2020 20:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:03: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:45:04: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 20:45:04: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 20:45:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:04: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 20:45:04: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 21 Jun 2020 20:45:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.20_model.r WARNING @ Sun, 21 Jun 2020 20:45:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:04: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 21 Jun 2020 20:45:04: #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 20:45:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:45:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375829/SRX4375829.20_summits.bed INFO @ Sun, 21 Jun 2020 20:45:27: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 6 millis CompletedMACS2peakCalling