Job ID = 6458390 SRX = SRX511130 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:28:19 prefetch.2.10.7: 1) Downloading 'SRR1217235'... 2020-06-21T12:28:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:29:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:29:55 prefetch.2.10.7: 'SRR1217235' is valid 2020-06-21T12:29:55 prefetch.2.10.7: 1) 'SRR1217235' was downloaded successfully Read 8214435 spots for SRR1217235/SRR1217235.sra Written 8214435 spots for SRR1217235/SRR1217235.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: 00:02:44 8214435 reads; of these: 8214435 (100.00%) were unpaired; of these: 215927 (2.63%) aligned 0 times 5131965 (62.47%) aligned exactly 1 time 2866543 (34.90%) aligned >1 times 97.37% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 837599 / 7998508 = 0.1047 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 21:35:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.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 21:35:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:48: 1000000 INFO @ Sun, 21 Jun 2020 21:35:54: 2000000 INFO @ Sun, 21 Jun 2020 21:35:59: 3000000 INFO @ Sun, 21 Jun 2020 21:36:05: 4000000 INFO @ Sun, 21 Jun 2020 21:36:10: 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 21:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.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 21:36:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:16: 6000000 INFO @ Sun, 21 Jun 2020 21:36:20: 1000000 INFO @ Sun, 21 Jun 2020 21:36:22: 7000000 INFO @ Sun, 21 Jun 2020 21:36:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:36:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:36:23: #1 total tags in treatment: 7160909 INFO @ Sun, 21 Jun 2020 21:36:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:23: #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 21:36:23: #1 tags after filtering in treatment: 7160777 INFO @ Sun, 21 Jun 2020 21:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:24: #2 number of paired peaks: 2433 INFO @ Sun, 21 Jun 2020 21:36:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:24: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:36:24: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 21:36:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.05_model.r WARNING @ Sun, 21 Jun 2020 21:36:24: #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 21:36:24: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 21:36:24: #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 21:36:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:26: 2000000 INFO @ Sun, 21 Jun 2020 21:36:32: 3000000 INFO @ Sun, 21 Jun 2020 21:36:39: 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 21:36:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.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 21:36:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:45: 5000000 INFO @ Sun, 21 Jun 2020 21:36:49: 1000000 INFO @ Sun, 21 Jun 2020 21:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.05_summits.bed INFO @ Sun, 21 Jun 2020 21:36:50: Done! pass1 - making usageList (541 chroms): 1 millis pass2 - checking and writing primary data (2511 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:51: 6000000 INFO @ Sun, 21 Jun 2020 21:36:55: 2000000 INFO @ Sun, 21 Jun 2020 21:36:58: 7000000 INFO @ Sun, 21 Jun 2020 21:36:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:36:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:36:59: #1 total tags in treatment: 7160909 INFO @ Sun, 21 Jun 2020 21:36:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:59: #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 21:36:59: #1 tags after filtering in treatment: 7160777 INFO @ Sun, 21 Jun 2020 21:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:59: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:00: #2 number of paired peaks: 2433 INFO @ Sun, 21 Jun 2020 21:37:00: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:00: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:00: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:00: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:00: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:37:00: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 21:37:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.10_model.r WARNING @ Sun, 21 Jun 2020 21:37:00: #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 21:37:00: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 21:37:00: #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 21:37:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:01: 3000000 INFO @ Sun, 21 Jun 2020 21:37:07: 4000000 INFO @ Sun, 21 Jun 2020 21:37:13: 5000000 INFO @ Sun, 21 Jun 2020 21:37:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:19: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.10_summits.bed INFO @ Sun, 21 Jun 2020 21:37:25: Done! pass1 - making usageList (465 chroms): 1 millis pass2 - checking and writing primary data (1674 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:37:25: 7000000 INFO @ Sun, 21 Jun 2020 21:37:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:26: #1 total tags in treatment: 7160909 INFO @ Sun, 21 Jun 2020 21:37:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:26: #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 21:37:27: #1 tags after filtering in treatment: 7160777 INFO @ Sun, 21 Jun 2020 21:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:27: #2 number of paired peaks: 2433 INFO @ Sun, 21 Jun 2020 21:37:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:28: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:37:28: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 21:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.20_model.r WARNING @ Sun, 21 Jun 2020 21:37:28: #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 21:37:28: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 21:37:28: #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 21:37:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:37:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511130/SRX511130.20_summits.bed INFO @ Sun, 21 Jun 2020 21:37:51: Done! pass1 - making usageList (250 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 9 millis CompletedMACS2peakCalling