Job ID = 6453113 SRX = SRX1032412 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:38 prefetch.2.10.7: 1) Downloading 'SRR2031913'... 2020-06-21T07:59:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:32 prefetch.2.10.7: 'SRR2031913' is valid 2020-06-21T08:01:32 prefetch.2.10.7: 1) 'SRR2031913' was downloaded successfully Read 13165326 spots for SRR2031913/SRR2031913.sra Written 13165326 spots for SRR2031913/SRR2031913.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: 00:03:01 13165326 reads; of these: 13165326 (100.00%) were unpaired; of these: 1045194 (7.94%) aligned 0 times 9453260 (71.80%) aligned exactly 1 time 2666872 (20.26%) aligned >1 times 92.06% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 4373899 / 12120132 = 0.3609 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 17:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.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 17:08:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:46: 1000000 INFO @ Sun, 21 Jun 2020 17:08:52: 2000000 INFO @ Sun, 21 Jun 2020 17:08:57: 3000000 INFO @ Sun, 21 Jun 2020 17:09:02: 4000000 INFO @ Sun, 21 Jun 2020 17:09:08: 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 17:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.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 17:09:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:13: 6000000 INFO @ Sun, 21 Jun 2020 17:09:16: 1000000 INFO @ Sun, 21 Jun 2020 17:09:19: 7000000 INFO @ Sun, 21 Jun 2020 17:09:21: 2000000 INFO @ Sun, 21 Jun 2020 17:09:23: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 17:09:23: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 17:09:23: #1 total tags in treatment: 7746233 INFO @ Sun, 21 Jun 2020 17:09:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:23: #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 17:09:24: #1 tags after filtering in treatment: 7746208 INFO @ Sun, 21 Jun 2020 17:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:25: #2 number of paired peaks: 1500 INFO @ Sun, 21 Jun 2020 17:09:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:25: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:09:25: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 21 Jun 2020 17:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.05_model.r WARNING @ Sun, 21 Jun 2020 17:09:25: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:25: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 21 Jun 2020 17:09:25: #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 17:09:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:27: 3000000 INFO @ Sun, 21 Jun 2020 17:09:32: 4000000 INFO @ Sun, 21 Jun 2020 17:09:37: 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 17:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.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 17:09:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:43: 6000000 INFO @ Sun, 21 Jun 2020 17:09:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:46: 1000000 INFO @ Sun, 21 Jun 2020 17:09:49: 7000000 INFO @ Sun, 21 Jun 2020 17:09:52: 2000000 INFO @ Sun, 21 Jun 2020 17:09:53: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 17:09:53: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 17:09:53: #1 total tags in treatment: 7746233 INFO @ Sun, 21 Jun 2020 17:09:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:53: #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 17:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.05_summits.bed INFO @ Sun, 21 Jun 2020 17:09:53: Done! INFO @ Sun, 21 Jun 2020 17:09:53: #1 tags after filtering in treatment: 7746208 INFO @ Sun, 21 Jun 2020 17:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:53: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (323 chroms): 2 millis pass2 - checking and writing primary data (3887 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:54: #2 number of paired peaks: 1500 INFO @ Sun, 21 Jun 2020 17:09:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:54: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:09:54: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 21 Jun 2020 17:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.10_model.r WARNING @ Sun, 21 Jun 2020 17:09:54: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:54: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 21 Jun 2020 17:09:54: #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 17:09:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:57: 3000000 INFO @ Sun, 21 Jun 2020 17:10:02: 4000000 INFO @ Sun, 21 Jun 2020 17:10:07: 5000000 INFO @ Sun, 21 Jun 2020 17:10:13: 6000000 INFO @ Sun, 21 Jun 2020 17:10:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:19: 7000000 INFO @ Sun, 21 Jun 2020 17:10:23: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 17:10:23: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 17:10:23: #1 total tags in treatment: 7746233 INFO @ Sun, 21 Jun 2020 17:10:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:23: #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 17:10:24: #1 tags after filtering in treatment: 7746208 INFO @ Sun, 21 Jun 2020 17:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:24: #2 number of paired peaks: 1500 INFO @ Sun, 21 Jun 2020 17:10:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:24: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:10:24: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 21 Jun 2020 17:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.20_model.r WARNING @ Sun, 21 Jun 2020 17:10:24: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:10:24: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 21 Jun 2020 17:10:24: #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 17:10:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:24: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (2138 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:10:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032412/SRX1032412.20_summits.bed INFO @ Sun, 21 Jun 2020 17:10:54: Done! pass1 - making usageList (154 chroms): 1 millis pass2 - checking and writing primary data (1410 records, 4 fields): 9 millis CompletedMACS2peakCalling