Job ID = 6454503 SRX = SRX2165287 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:39 prefetch.2.10.7: 1) Downloading 'SRR4244803'... 2020-06-21T09:06:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:12:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:12:17 prefetch.2.10.7: 1) 'SRR4244803' was downloaded successfully Read 26248602 spots for SRR4244803/SRR4244803.sra Written 26248602 spots for SRR4244803/SRR4244803.sra 2020-06-21T09:14:02 prefetch.2.10.7: 1) Downloading 'SRR4244804'... 2020-06-21T09:14:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:19:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:19:56 prefetch.2.10.7: 1) 'SRR4244804' was downloaded successfully Read 25235086 spots for SRR4244804/SRR4244804.sra Written 25235086 spots for SRR4244804/SRR4244804.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: 00:00:01 Multiseed full-index search: 00:17:10 51483688 reads; of these: 51483688 (100.00%) were unpaired; of these: 6154944 (11.96%) aligned 0 times 32957748 (64.02%) aligned exactly 1 time 12370996 (24.03%) aligned >1 times 88.04% overall alignment rate Time searching: 00:17:11 Overall time: 00:17:11 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 20 files... [bam_rmdupse_core] 38790549 / 45328744 = 0.8558 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 18:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.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 18:49:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:23: 1000000 INFO @ Sun, 21 Jun 2020 18:49:29: 2000000 INFO @ Sun, 21 Jun 2020 18:49:35: 3000000 INFO @ Sun, 21 Jun 2020 18:49:41: 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 18:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.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 18:49:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:49: 5000000 INFO @ Sun, 21 Jun 2020 18:49:54: 1000000 INFO @ Sun, 21 Jun 2020 18:49:56: 6000000 INFO @ Sun, 21 Jun 2020 18:50:00: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:50:00: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:50:00: #1 total tags in treatment: 6538195 INFO @ Sun, 21 Jun 2020 18:50:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:00: #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 18:50:00: #1 tags after filtering in treatment: 6538190 INFO @ Sun, 21 Jun 2020 18:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:00: 2000000 INFO @ Sun, 21 Jun 2020 18:50:01: #2 number of paired peaks: 3774 INFO @ Sun, 21 Jun 2020 18:50:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:01: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 18:50:01: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 18:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.05_model.r WARNING @ Sun, 21 Jun 2020 18:50:01: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:01: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 18:50:01: #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 18:50:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:07: 3000000 INFO @ Sun, 21 Jun 2020 18:50:13: 4000000 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 18:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.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 18:50:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:20: 5000000 INFO @ Sun, 21 Jun 2020 18:50:23: 1000000 INFO @ Sun, 21 Jun 2020 18:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:25: Done! pass1 - making usageList (1000 chroms): 3 millis pass2 - checking and writing primary data (7239 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:27: 6000000 INFO @ Sun, 21 Jun 2020 18:50:30: 2000000 INFO @ Sun, 21 Jun 2020 18:50:31: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:50:31: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:50:31: #1 total tags in treatment: 6538195 INFO @ Sun, 21 Jun 2020 18:50:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:31: #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 18:50:32: #1 tags after filtering in treatment: 6538190 INFO @ Sun, 21 Jun 2020 18:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:32: #2 number of paired peaks: 3774 INFO @ Sun, 21 Jun 2020 18:50:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:33: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 18:50:33: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 18:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.10_model.r WARNING @ Sun, 21 Jun 2020 18:50:33: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:33: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 18:50:33: #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 18:50:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:36: 3000000 INFO @ Sun, 21 Jun 2020 18:50:42: 4000000 INFO @ Sun, 21 Jun 2020 18:50:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:56: 6000000 INFO @ Sun, 21 Jun 2020 18:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.10_summits.bed INFO @ Sun, 21 Jun 2020 18:50:56: Done! pass1 - making usageList (755 chroms): 2 millis pass2 - checking and writing primary data (3886 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:59: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:50:59: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:50:59: #1 total tags in treatment: 6538195 INFO @ Sun, 21 Jun 2020 18:50:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:59: #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 18:51:00: #1 tags after filtering in treatment: 6538190 INFO @ Sun, 21 Jun 2020 18:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:00: #2 number of paired peaks: 3774 INFO @ Sun, 21 Jun 2020 18:51:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:01: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 18:51:01: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 18:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.20_model.r WARNING @ Sun, 21 Jun 2020 18:51:01: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:01: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 18:51:01: #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 18:51:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165287/SRX2165287.20_summits.bed INFO @ Sun, 21 Jun 2020 18:51:24: Done! pass1 - making usageList (594 chroms): 2 millis pass2 - checking and writing primary data (2333 records, 4 fields): 33 millis CompletedMACS2peakCalling