Job ID = 6453266 SRX = SRX110780 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:19:32 prefetch.2.10.7: 1) Downloading 'SRR388362'... 2020-06-21T08:19:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:30 prefetch.2.10.7: 'SRR388362' is valid 2020-06-21T08:21:30 prefetch.2.10.7: 1) 'SRR388362' was downloaded successfully Read 10901385 spots for SRR388362/SRR388362.sra Written 10901385 spots for SRR388362/SRR388362.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: 00:02:19 10901385 reads; of these: 10901385 (100.00%) were unpaired; of these: 662509 (6.08%) aligned 0 times 7573539 (69.47%) aligned exactly 1 time 2665337 (24.45%) aligned >1 times 93.92% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 841347 / 10238876 = 0.0822 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 17:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.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 17:27:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:30: 1000000 INFO @ Sun, 21 Jun 2020 17:27:35: 2000000 INFO @ Sun, 21 Jun 2020 17:27:41: 3000000 INFO @ Sun, 21 Jun 2020 17:27:47: 4000000 INFO @ Sun, 21 Jun 2020 17:27:52: 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 17:27:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.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 17:27:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:59: 6000000 INFO @ Sun, 21 Jun 2020 17:28:01: 1000000 INFO @ Sun, 21 Jun 2020 17:28:05: 7000000 INFO @ Sun, 21 Jun 2020 17:28:07: 2000000 INFO @ Sun, 21 Jun 2020 17:28:12: 8000000 INFO @ Sun, 21 Jun 2020 17:28:13: 3000000 INFO @ Sun, 21 Jun 2020 17:28:18: 9000000 INFO @ Sun, 21 Jun 2020 17:28:20: 4000000 INFO @ Sun, 21 Jun 2020 17:28:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:28:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:28:21: #1 total tags in treatment: 9397529 INFO @ Sun, 21 Jun 2020 17:28:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:21: #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 17:28:21: #1 tags after filtering in treatment: 9397526 INFO @ Sun, 21 Jun 2020 17:28:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:22: #2 number of paired peaks: 2295 INFO @ Sun, 21 Jun 2020 17:28:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:22: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 17:28:22: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 21 Jun 2020 17:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.05_model.r WARNING @ Sun, 21 Jun 2020 17:28:22: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:28:22: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sun, 21 Jun 2020 17:28:22: #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 17:28:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:22: #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 17:28:25: 5000000 INFO @ Sun, 21 Jun 2020 17:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.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 17:28:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:32: 6000000 INFO @ Sun, 21 Jun 2020 17:28:32: 1000000 INFO @ Sun, 21 Jun 2020 17:28:38: 7000000 INFO @ Sun, 21 Jun 2020 17:28:39: 2000000 INFO @ Sun, 21 Jun 2020 17:28:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:45: 8000000 INFO @ Sun, 21 Jun 2020 17:28:45: 3000000 INFO @ Sun, 21 Jun 2020 17:28:51: 9000000 INFO @ Sun, 21 Jun 2020 17:28:51: 4000000 INFO @ Sun, 21 Jun 2020 17:28:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.05_summits.bed INFO @ Sun, 21 Jun 2020 17:28:54: Done! INFO @ Sun, 21 Jun 2020 17:28:54: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:28:54: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:28:54: #1 total tags in treatment: 9397529 INFO @ Sun, 21 Jun 2020 17:28:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (541 chroms): 1 millis pass2 - checking and writing primary data (3794 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:28:54: #1 tags after filtering in treatment: 9397526 INFO @ Sun, 21 Jun 2020 17:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:55: #2 number of paired peaks: 2295 INFO @ Sun, 21 Jun 2020 17:28:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:55: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 17:28:55: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 21 Jun 2020 17:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.10_model.r WARNING @ Sun, 21 Jun 2020 17:28:55: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:28:55: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sun, 21 Jun 2020 17:28:55: #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 17:28:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:57: 5000000 INFO @ Sun, 21 Jun 2020 17:29:03: 6000000 INFO @ Sun, 21 Jun 2020 17:29:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:15: 8000000 INFO @ Sun, 21 Jun 2020 17:29:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:21: 9000000 INFO @ Sun, 21 Jun 2020 17:29:23: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:29:23: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:29:23: #1 total tags in treatment: 9397529 INFO @ Sun, 21 Jun 2020 17:29:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:23: #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 17:29:23: #1 tags after filtering in treatment: 9397526 INFO @ Sun, 21 Jun 2020 17:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:24: #2 number of paired peaks: 2295 INFO @ Sun, 21 Jun 2020 17:29:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:24: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 17:29:24: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 21 Jun 2020 17:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.20_model.r WARNING @ Sun, 21 Jun 2020 17:29:24: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:29:24: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sun, 21 Jun 2020 17:29:24: #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 17:29:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.10_summits.bed INFO @ Sun, 21 Jun 2020 17:29:28: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (1498 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110780/SRX110780.20_summits.bed INFO @ Sun, 21 Jun 2020 17:29:56: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 6 millis CompletedMACS2peakCalling