Job ID = 6452662 SRX = SRX025470 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:43:36 prefetch.2.10.7: 1) Downloading 'SRR063864'... 2020-06-21T07:43:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:11 prefetch.2.10.7: 'SRR063864' is valid 2020-06-21T07:44:11 prefetch.2.10.7: 1) 'SRR063864' was downloaded successfully Read 8794379 spots for SRR063864/SRR063864.sra Written 8794379 spots for SRR063864/SRR063864.sra 2020-06-21T07:44:44 prefetch.2.10.7: 1) Downloading 'SRR063865'... 2020-06-21T07:44:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:45:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:45:33 prefetch.2.10.7: 'SRR063865' is valid 2020-06-21T07:45:33 prefetch.2.10.7: 1) 'SRR063865' was downloaded successfully Read 6611077 spots for SRR063865/SRR063865.sra Written 6611077 spots for SRR063865/SRR063865.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: 00:05:03 15405456 reads; of these: 15405456 (100.00%) were unpaired; of these: 2175107 (14.12%) aligned 0 times 5535382 (35.93%) aligned exactly 1 time 7694967 (49.95%) aligned >1 times 85.88% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 8493669 / 13230349 = 0.6420 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 16:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.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 16:53:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:16: 1000000 INFO @ Sun, 21 Jun 2020 16:53:21: 2000000 INFO @ Sun, 21 Jun 2020 16:53:27: 3000000 INFO @ Sun, 21 Jun 2020 16:53:32: 4000000 INFO @ Sun, 21 Jun 2020 16:53:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:36: #1 total tags in treatment: 4736680 INFO @ Sun, 21 Jun 2020 16:53:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:36: #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 16:53:36: #1 tags after filtering in treatment: 4736661 INFO @ Sun, 21 Jun 2020 16:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:36: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:37: #2 number of paired peaks: 2772 INFO @ Sun, 21 Jun 2020 16:53:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:37: #2 predicted fragment length is 34 bps INFO @ Sun, 21 Jun 2020 16:53:37: #2 alternative fragment length(s) may be 3,34 bps INFO @ Sun, 21 Jun 2020 16:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.05_model.r WARNING @ Sun, 21 Jun 2020 16:53:37: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:53:37: #2 You may need to consider one of the other alternative d(s): 3,34 WARNING @ Sun, 21 Jun 2020 16:53:37: #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 16:53:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:37: #3 Pre-compute pvalue-qvalue table... 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 16:53:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.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 16:53:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:45: 1000000 INFO @ Sun, 21 Jun 2020 16:53:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:50: 2000000 INFO @ Sun, 21 Jun 2020 16:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.05_summits.bed INFO @ Sun, 21 Jun 2020 16:53:51: Done! pass1 - making usageList (748 chroms): 2 millis pass2 - checking and writing primary data (3341 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:53:54: 3000000 INFO @ Sun, 21 Jun 2020 16:53:59: 4000000 INFO @ Sun, 21 Jun 2020 16:54:02: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:02: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:02: #1 total tags in treatment: 4736680 INFO @ Sun, 21 Jun 2020 16:54:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:02: #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 16:54:03: #1 tags after filtering in treatment: 4736661 INFO @ Sun, 21 Jun 2020 16:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:03: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:03: #2 number of paired peaks: 2772 INFO @ Sun, 21 Jun 2020 16:54:03: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:03: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:03: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:03: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:03: #2 predicted fragment length is 34 bps INFO @ Sun, 21 Jun 2020 16:54:03: #2 alternative fragment length(s) may be 3,34 bps INFO @ Sun, 21 Jun 2020 16:54:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.10_model.r WARNING @ Sun, 21 Jun 2020 16:54:03: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:03: #2 You may need to consider one of the other alternative d(s): 3,34 WARNING @ Sun, 21 Jun 2020 16:54:03: #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 16:54:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:03: #3 Pre-compute pvalue-qvalue table... 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 16:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.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 16:54:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:15: 1000000 INFO @ Sun, 21 Jun 2020 16:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.10_summits.bed INFO @ Sun, 21 Jun 2020 16:54:17: Done! pass1 - making usageList (592 chroms): 1 millis pass2 - checking and writing primary data (2466 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:20: 2000000 INFO @ Sun, 21 Jun 2020 16:54:24: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:54:29: 4000000 INFO @ Sun, 21 Jun 2020 16:54:33: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:33: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:33: #1 total tags in treatment: 4736680 INFO @ Sun, 21 Jun 2020 16:54:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:33: #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 16:54:33: #1 tags after filtering in treatment: 4736661 INFO @ Sun, 21 Jun 2020 16:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:33: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:33: #2 number of paired peaks: 2772 INFO @ Sun, 21 Jun 2020 16:54:33: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:33: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:33: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:33: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:33: #2 predicted fragment length is 34 bps INFO @ Sun, 21 Jun 2020 16:54:33: #2 alternative fragment length(s) may be 3,34 bps INFO @ Sun, 21 Jun 2020 16:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.20_model.r WARNING @ Sun, 21 Jun 2020 16:54:33: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:33: #2 You may need to consider one of the other alternative d(s): 3,34 WARNING @ Sun, 21 Jun 2020 16:54:33: #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 16:54:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:54:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025470/SRX025470.20_summits.bed INFO @ Sun, 21 Jun 2020 16:54:47: Done! pass1 - making usageList (450 chroms): 1 millis pass2 - checking and writing primary data (1979 records, 4 fields): 14 millis CompletedMACS2peakCalling