Job ID = 6454745 SRX = SRX2564128 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:26:14 prefetch.2.10.7: 1) Downloading 'SRR5259249'... 2020-06-21T09:26:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:29:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:29:10 prefetch.2.10.7: 'SRR5259249' is valid 2020-06-21T09:29:10 prefetch.2.10.7: 1) 'SRR5259249' was downloaded successfully Read 22142303 spots for SRR5259249/SRR5259249.sra Written 22142303 spots for SRR5259249/SRR5259249.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: 00:02:45 22142303 reads; of these: 22142303 (100.00%) were unpaired; of these: 16710960 (75.47%) aligned 0 times 3870105 (17.48%) aligned exactly 1 time 1561238 (7.05%) aligned >1 times 24.53% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1738085 / 5431343 = 0.3200 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 18:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.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 18:34:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:49: 1000000 INFO @ Sun, 21 Jun 2020 18:34:55: 2000000 INFO @ Sun, 21 Jun 2020 18:35:00: 3000000 INFO @ Sun, 21 Jun 2020 18:35:04: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:35:04: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:35:04: #1 total tags in treatment: 3693258 INFO @ Sun, 21 Jun 2020 18:35:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:04: #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 18:35:05: #1 tags after filtering in treatment: 3693091 INFO @ Sun, 21 Jun 2020 18:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:05: #2 number of paired peaks: 1859 INFO @ Sun, 21 Jun 2020 18:35:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:05: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:35:05: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 21 Jun 2020 18:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.05_model.r WARNING @ Sun, 21 Jun 2020 18:35:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:05: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 21 Jun 2020 18:35:05: #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 18:35:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:05: #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 @ Sun, 21 Jun 2020 18:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.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 18:35:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:18: Done! INFO @ Sun, 21 Jun 2020 18:35:19: 1000000 pass1 - making usageList (398 chroms): 2 millis pass2 - checking and writing primary data (3073 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:25: 2000000 INFO @ Sun, 21 Jun 2020 18:35:30: 3000000 INFO @ Sun, 21 Jun 2020 18:35:35: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:35:35: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:35:35: #1 total tags in treatment: 3693258 INFO @ Sun, 21 Jun 2020 18:35:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:35: #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 18:35:35: #1 tags after filtering in treatment: 3693091 INFO @ Sun, 21 Jun 2020 18:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:35: #2 number of paired peaks: 1859 INFO @ Sun, 21 Jun 2020 18:35:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:35: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:35:35: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 21 Jun 2020 18:35:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.10_model.r WARNING @ Sun, 21 Jun 2020 18:35:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:35: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 21 Jun 2020 18:35:35: #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 18:35:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:35: #3 Pre-compute pvalue-qvalue table... 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 18:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.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 18:35:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:48: Done! pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:51: 1000000 INFO @ Sun, 21 Jun 2020 18:35:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:36:04: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:36:09: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:36:09: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:36:09: #1 total tags in treatment: 3693258 INFO @ Sun, 21 Jun 2020 18:36:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:09: #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 18:36:09: #1 tags after filtering in treatment: 3693091 INFO @ Sun, 21 Jun 2020 18:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:10: #2 number of paired peaks: 1859 INFO @ Sun, 21 Jun 2020 18:36:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:10: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:36:10: #2 alternative fragment length(s) may be 52 bps INFO @ Sun, 21 Jun 2020 18:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.20_model.r WARNING @ Sun, 21 Jun 2020 18:36:10: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:36:10: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sun, 21 Jun 2020 18:36:10: #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 18:36:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564128/SRX2564128.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:23: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (542 records, 4 fields): 7 millis CompletedMACS2peakCalling