Job ID = 6454673 SRX = SRX2458934 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:10 prefetch.2.10.7: 1) Downloading 'SRR5140283'... 2020-06-21T09:35:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:38:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:38:08 prefetch.2.10.7: 1) 'SRR5140283' was downloaded successfully Read 20075401 spots for SRR5140283/SRR5140283.sra Written 20075401 spots for SRR5140283/SRR5140283.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: 00:04:49 20075401 reads; of these: 20075401 (100.00%) were unpaired; of these: 2239604 (11.16%) aligned 0 times 12561167 (62.57%) aligned exactly 1 time 5274630 (26.27%) aligned >1 times 88.84% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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 8 files... [bam_rmdupse_core] 6932050 / 17835797 = 0.3887 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 18:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.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 18:48:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:30: 1000000 INFO @ Sun, 21 Jun 2020 18:48:37: 2000000 INFO @ Sun, 21 Jun 2020 18:48:43: 3000000 INFO @ Sun, 21 Jun 2020 18:48:49: 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 18:48:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.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 18:48:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:55: 5000000 INFO @ Sun, 21 Jun 2020 18:49:00: 1000000 INFO @ Sun, 21 Jun 2020 18:49:02: 6000000 INFO @ Sun, 21 Jun 2020 18:49:05: 2000000 INFO @ Sun, 21 Jun 2020 18:49:09: 7000000 INFO @ Sun, 21 Jun 2020 18:49:11: 3000000 INFO @ Sun, 21 Jun 2020 18:49:15: 8000000 INFO @ Sun, 21 Jun 2020 18:49:16: 4000000 INFO @ Sun, 21 Jun 2020 18:49:22: 5000000 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 18:49:22: 9000000 INFO @ Sun, 21 Jun 2020 18:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.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 18:49:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:27: 6000000 INFO @ Sun, 21 Jun 2020 18:49:29: 10000000 INFO @ Sun, 21 Jun 2020 18:49:30: 1000000 INFO @ Sun, 21 Jun 2020 18:49:33: 7000000 INFO @ Sun, 21 Jun 2020 18:49:35: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:49:35: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:49:35: #1 total tags in treatment: 10903747 INFO @ Sun, 21 Jun 2020 18:49:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:35: #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 18:49:35: 2000000 INFO @ Sun, 21 Jun 2020 18:49:35: #1 tags after filtering in treatment: 10903683 INFO @ Sun, 21 Jun 2020 18:49:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:36: #2 number of paired peaks: 2187 INFO @ Sun, 21 Jun 2020 18:49:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:36: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:49:36: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.05_model.r WARNING @ Sun, 21 Jun 2020 18:49:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:36: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:49:36: #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 18:49:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:39: 8000000 INFO @ Sun, 21 Jun 2020 18:49:41: 3000000 INFO @ Sun, 21 Jun 2020 18:49:45: 9000000 INFO @ Sun, 21 Jun 2020 18:49:46: 4000000 INFO @ Sun, 21 Jun 2020 18:49:50: 10000000 INFO @ Sun, 21 Jun 2020 18:49:52: 5000000 INFO @ Sun, 21 Jun 2020 18:49:56: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:49:56: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:49:56: #1 total tags in treatment: 10903747 INFO @ Sun, 21 Jun 2020 18:49:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:56: #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 18:49:56: #1 tags after filtering in treatment: 10903683 INFO @ Sun, 21 Jun 2020 18:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:57: #2 number of paired peaks: 2187 INFO @ Sun, 21 Jun 2020 18:49:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:57: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:49:57: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.10_model.r WARNING @ Sun, 21 Jun 2020 18:49:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:57: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:49:57: #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 18:49:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:58: 6000000 INFO @ Sun, 21 Jun 2020 18:50:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:03: 7000000 INFO @ Sun, 21 Jun 2020 18:50:09: 8000000 INFO @ Sun, 21 Jun 2020 18:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:12: Done! pass1 - making usageList (720 chroms): 2 millis pass2 - checking and writing primary data (3296 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:15: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:20: 10000000 INFO @ Sun, 21 Jun 2020 18:50:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:25: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:50:25: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:50:25: #1 total tags in treatment: 10903747 INFO @ Sun, 21 Jun 2020 18:50:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:25: #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 18:50:26: #1 tags after filtering in treatment: 10903683 INFO @ Sun, 21 Jun 2020 18:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:27: #2 number of paired peaks: 2187 INFO @ Sun, 21 Jun 2020 18:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:27: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:50:27: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.20_model.r WARNING @ Sun, 21 Jun 2020 18:50:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:27: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:50:27: #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 18:50:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.10_summits.bed INFO @ Sun, 21 Jun 2020 18:50:33: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (2256 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458934/SRX2458934.20_summits.bed INFO @ Sun, 21 Jun 2020 18:51:02: Done! pass1 - making usageList (401 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 13 millis CompletedMACS2peakCalling