Job ID = 6457262 SRX = SRX4639142 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:38:12 prefetch.2.10.7: 1) Downloading 'SRR7784123'... 2020-06-21T11:38:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:49:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:49:06 prefetch.2.10.7: 1) 'SRR7784123' was downloaded successfully Read 50555435 spots for SRR7784123/SRR7784123.sra Written 50555435 spots for SRR7784123/SRR7784123.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: 00:09:43 50555435 reads; of these: 50555435 (100.00%) were unpaired; of these: 29723809 (58.79%) aligned 0 times 15527052 (30.71%) aligned exactly 1 time 5304574 (10.49%) aligned >1 times 41.21% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 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_sort_core] merging from 12 files... [bam_rmdupse_core] 16777281 / 20831626 = 0.8054 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 21:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.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 21:05:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:03: 1000000 INFO @ Sun, 21 Jun 2020 21:06:09: 2000000 INFO @ Sun, 21 Jun 2020 21:06:15: 3000000 INFO @ Sun, 21 Jun 2020 21:06:21: 4000000 INFO @ Sun, 21 Jun 2020 21:06:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:06:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:06:22: #1 total tags in treatment: 4054345 INFO @ Sun, 21 Jun 2020 21:06:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:22: #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 21:06:22: #1 tags after filtering in treatment: 4054306 INFO @ Sun, 21 Jun 2020 21:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:23: #2 number of paired peaks: 2636 INFO @ Sun, 21 Jun 2020 21:06:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:23: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:06:23: #2 alternative fragment length(s) may be 3,54,571 bps INFO @ Sun, 21 Jun 2020 21:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.05_model.r WARNING @ Sun, 21 Jun 2020 21:06:23: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:06:23: #2 You may need to consider one of the other alternative d(s): 3,54,571 WARNING @ Sun, 21 Jun 2020 21:06:23: #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 21:06:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:23: #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 21:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.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 21:06:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:06:34: 1000000 INFO @ Sun, 21 Jun 2020 21:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.05_summits.bed INFO @ Sun, 21 Jun 2020 21:06:36: Done! pass1 - making usageList (739 chroms): 1 millis pass2 - checking and writing primary data (3106 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:06:41: 2000000 INFO @ Sun, 21 Jun 2020 21:06:48: 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 21:06:55: 4000000 INFO @ Sun, 21 Jun 2020 21:06:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:06:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:06:56: #1 total tags in treatment: 4054345 INFO @ Sun, 21 Jun 2020 21:06:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:56: #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 21:06:56: #1 tags after filtering in treatment: 4054306 INFO @ Sun, 21 Jun 2020 21:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:56: #2 number of paired peaks: 2636 INFO @ Sun, 21 Jun 2020 21:06:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:57: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:06:57: #2 alternative fragment length(s) may be 3,54,571 bps INFO @ Sun, 21 Jun 2020 21:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.10_model.r WARNING @ Sun, 21 Jun 2020 21:06:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:06:57: #2 You may need to consider one of the other alternative d(s): 3,54,571 WARNING @ Sun, 21 Jun 2020 21:06:57: #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 21:06:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.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 21:06:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:05: 1000000 INFO @ Sun, 21 Jun 2020 21:07:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:07:12: 2000000 INFO @ Sun, 21 Jun 2020 21:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.10_summits.bed INFO @ Sun, 21 Jun 2020 21:07:12: Done! pass1 - making usageList (609 chroms): 2 millis pass2 - checking and writing primary data (2406 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:07:19: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:07:27: 4000000 INFO @ Sun, 21 Jun 2020 21:07:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:07:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:07:27: #1 total tags in treatment: 4054345 INFO @ Sun, 21 Jun 2020 21:07:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:27: #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 21:07:27: #1 tags after filtering in treatment: 4054306 INFO @ Sun, 21 Jun 2020 21:07:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:28: #2 number of paired peaks: 2636 INFO @ Sun, 21 Jun 2020 21:07:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:28: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 21:07:28: #2 alternative fragment length(s) may be 3,54,571 bps INFO @ Sun, 21 Jun 2020 21:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.20_model.r WARNING @ Sun, 21 Jun 2020 21:07:28: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:28: #2 You may need to consider one of the other alternative d(s): 3,54,571 WARNING @ Sun, 21 Jun 2020 21:07:28: #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 21:07:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639142/SRX4639142.20_summits.bed INFO @ Sun, 21 Jun 2020 21:07:42: Done! pass1 - making usageList (515 chroms): 2 millis pass2 - checking and writing primary data (1597 records, 4 fields): 21 millis CompletedMACS2peakCalling