Job ID = 6453607 SRX = SRX1299933 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:39:47 prefetch.2.10.7: 1) Downloading 'SRR2546852'... 2020-06-21T08:39:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:31 prefetch.2.10.7: 'SRR2546852' is valid 2020-06-21T08:43:31 prefetch.2.10.7: 1) 'SRR2546852' was downloaded successfully Read 10651616 spots for SRR2546852/SRR2546852.sra Written 10651616 spots for SRR2546852/SRR2546852.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: 00:02:58 10651616 reads; of these: 10651616 (100.00%) were unpaired; of these: 2956119 (27.75%) aligned 0 times 4683059 (43.97%) aligned exactly 1 time 3012438 (28.28%) aligned >1 times 72.25% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 2884017 / 7695497 = 0.3748 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 17:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.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 17:49:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:58: 1000000 INFO @ Sun, 21 Jun 2020 17:50:05: 2000000 INFO @ Sun, 21 Jun 2020 17:50:12: 3000000 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 17:50:20: 4000000 INFO @ Sun, 21 Jun 2020 17:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.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 17:50:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:27: #1 total tags in treatment: 4811480 INFO @ Sun, 21 Jun 2020 17:50:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:27: #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 17:50:27: #1 tags after filtering in treatment: 4811360 INFO @ Sun, 21 Jun 2020 17:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:28: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 17:50:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:28: 1000000 INFO @ Sun, 21 Jun 2020 17:50:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:28: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 17:50:28: #2 alternative fragment length(s) may be 4,73,77 bps INFO @ Sun, 21 Jun 2020 17:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.05_model.r WARNING @ Sun, 21 Jun 2020 17:50:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:28: #2 You may need to consider one of the other alternative d(s): 4,73,77 WARNING @ Sun, 21 Jun 2020 17:50:28: #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 17:50:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:35: 2000000 INFO @ Sun, 21 Jun 2020 17:50:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:42: 3000000 INFO @ Sun, 21 Jun 2020 17:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.05_summits.bed INFO @ Sun, 21 Jun 2020 17:50:45: Done! pass1 - making usageList (686 chroms): 2 millis pass2 - checking and writing primary data (2628 records, 4 fields): 39 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 17:50:50: 4000000 INFO @ Sun, 21 Jun 2020 17:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.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 17:50:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:57: #1 total tags in treatment: 4811480 INFO @ Sun, 21 Jun 2020 17:50:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:57: #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 17:50:57: #1 tags after filtering in treatment: 4811360 INFO @ Sun, 21 Jun 2020 17:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:58: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 17:50:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:58: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 17:50:58: #2 alternative fragment length(s) may be 4,73,77 bps INFO @ Sun, 21 Jun 2020 17:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.10_model.r WARNING @ Sun, 21 Jun 2020 17:50:58: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:58: #2 You may need to consider one of the other alternative d(s): 4,73,77 WARNING @ Sun, 21 Jun 2020 17:50:58: #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 17:50:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:58: 1000000 INFO @ Sun, 21 Jun 2020 17:51:05: 2000000 INFO @ Sun, 21 Jun 2020 17:51:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:12: 3000000 INFO @ Sun, 21 Jun 2020 17:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.10_summits.bed INFO @ Sun, 21 Jun 2020 17:51:15: Done! pass1 - making usageList (524 chroms): 2 millis pass2 - checking and writing primary data (1336 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:51:20: 4000000 INFO @ Sun, 21 Jun 2020 17:51:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:51:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:51:26: #1 total tags in treatment: 4811480 INFO @ Sun, 21 Jun 2020 17:51:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:26: #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 17:51:26: #1 tags after filtering in treatment: 4811360 INFO @ Sun, 21 Jun 2020 17:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:27: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 17:51:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:27: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 17:51:27: #2 alternative fragment length(s) may be 4,73,77 bps INFO @ Sun, 21 Jun 2020 17:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.20_model.r WARNING @ Sun, 21 Jun 2020 17:51:27: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:27: #2 You may need to consider one of the other alternative d(s): 4,73,77 WARNING @ Sun, 21 Jun 2020 17:51:27: #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 17:51:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:51:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299933/SRX1299933.20_summits.bed INFO @ Sun, 21 Jun 2020 17:51:43: Done! pass1 - making usageList (207 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 13 millis CompletedMACS2peakCalling