Job ID = 6453044 SRX = SRX101479 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:07:48 prefetch.2.10.7: 1) Downloading 'SRR353683'... 2020-06-21T08:07:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:14:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:14:07 prefetch.2.10.7: 1) 'SRR353683' was downloaded successfully Read 38092752 spots for SRR353683/SRR353683.sra Written 38092752 spots for SRR353683/SRR353683.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:26 38092752 reads; of these: 38092752 (100.00%) were unpaired; of these: 10247548 (26.90%) aligned 0 times 22396630 (58.79%) aligned exactly 1 time 5448574 (14.30%) aligned >1 times 73.10% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 17255912 / 27845204 = 0.6197 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 17:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.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 17:26:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:26:53: 1000000 INFO @ Sun, 21 Jun 2020 17:26:58: 2000000 INFO @ Sun, 21 Jun 2020 17:27:03: 3000000 INFO @ Sun, 21 Jun 2020 17:27:09: 4000000 INFO @ Sun, 21 Jun 2020 17:27:14: 5000000 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 17:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.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 17:27:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:20: 6000000 INFO @ Sun, 21 Jun 2020 17:27:23: 1000000 INFO @ Sun, 21 Jun 2020 17:27:26: 7000000 INFO @ Sun, 21 Jun 2020 17:27:29: 2000000 INFO @ Sun, 21 Jun 2020 17:27:32: 8000000 INFO @ Sun, 21 Jun 2020 17:27:35: 3000000 INFO @ Sun, 21 Jun 2020 17:27:38: 9000000 INFO @ Sun, 21 Jun 2020 17:27:41: 4000000 INFO @ Sun, 21 Jun 2020 17:27:44: 10000000 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 17:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.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 17:27:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:47: 5000000 INFO @ Sun, 21 Jun 2020 17:27:48: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:27:48: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:27:48: #1 total tags in treatment: 10589292 INFO @ Sun, 21 Jun 2020 17:27:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:48: #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 17:27:48: #1 tags after filtering in treatment: 10589231 INFO @ Sun, 21 Jun 2020 17:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:27:49: #2 number of paired peaks: 1079 INFO @ Sun, 21 Jun 2020 17:27:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:49: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:27:49: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 17:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.05_model.r WARNING @ Sun, 21 Jun 2020 17:27:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:27:49: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 17:27:49: #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 17:27:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:27:53: 1000000 INFO @ Sun, 21 Jun 2020 17:27:54: 6000000 INFO @ Sun, 21 Jun 2020 17:27:59: 2000000 INFO @ Sun, 21 Jun 2020 17:28:00: 7000000 INFO @ Sun, 21 Jun 2020 17:28:05: 3000000 INFO @ Sun, 21 Jun 2020 17:28:06: 8000000 INFO @ Sun, 21 Jun 2020 17:28:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:11: 4000000 INFO @ Sun, 21 Jun 2020 17:28:12: 9000000 INFO @ Sun, 21 Jun 2020 17:28:17: 5000000 INFO @ Sun, 21 Jun 2020 17:28:18: 10000000 INFO @ Sun, 21 Jun 2020 17:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.05_summits.bed INFO @ Sun, 21 Jun 2020 17:28:20: Done! pass1 - making usageList (616 chroms): 1 millis pass2 - checking and writing primary data (3056 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:28:22: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:28:22: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:28:22: #1 total tags in treatment: 10589292 INFO @ Sun, 21 Jun 2020 17:28:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:22: #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 17:28:22: #1 tags after filtering in treatment: 10589231 INFO @ Sun, 21 Jun 2020 17:28:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:23: #2 number of paired peaks: 1079 INFO @ Sun, 21 Jun 2020 17:28:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:23: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:28:23: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 17:28:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.10_model.r WARNING @ Sun, 21 Jun 2020 17:28:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:28:23: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 17:28:23: #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 17:28:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:23: 6000000 INFO @ Sun, 21 Jun 2020 17:28:29: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:28:35: 8000000 INFO @ Sun, 21 Jun 2020 17:28:40: 9000000 INFO @ Sun, 21 Jun 2020 17:28:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:46: 10000000 INFO @ Sun, 21 Jun 2020 17:28:49: #1 tag size is determined as 41 bps INFO @ Sun, 21 Jun 2020 17:28:49: #1 tag size = 41 INFO @ Sun, 21 Jun 2020 17:28:49: #1 total tags in treatment: 10589292 INFO @ Sun, 21 Jun 2020 17:28:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:49: #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 17:28:49: #1 tags after filtering in treatment: 10589231 INFO @ Sun, 21 Jun 2020 17:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:50: #2 number of paired peaks: 1079 INFO @ Sun, 21 Jun 2020 17:28:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:50: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 17:28:50: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 17:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.20_model.r WARNING @ Sun, 21 Jun 2020 17:28:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:28:50: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 17:28:50: #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 17:28:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.10_peaks.xls BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.10_summits.bed INFO @ Sun, 21 Jun 2020 17:28:56: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (2164 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:29:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101479/SRX101479.20_summits.bed INFO @ Sun, 21 Jun 2020 17:29:22: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 9 millis CompletedMACS2peakCalling