Job ID = 6455123 SRX = SRX273676 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:06:25 prefetch.2.10.7: 1) Downloading 'SRR837793'... 2020-06-21T10:06:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:09:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:09:12 prefetch.2.10.7: 'SRR837793' is valid 2020-06-21T10:09:12 prefetch.2.10.7: 1) 'SRR837793' was downloaded successfully Read 8424939 spots for SRR837793/SRR837793.sra Written 8424939 spots for SRR837793/SRR837793.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: 00:03:22 8424939 reads; of these: 8424939 (100.00%) were unpaired; of these: 654070 (7.76%) aligned 0 times 5529616 (65.63%) aligned exactly 1 time 2241253 (26.60%) aligned >1 times 92.24% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 1865604 / 7770869 = 0.2401 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 19:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.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 19:16:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:44: 1000000 INFO @ Sun, 21 Jun 2020 19:16:51: 2000000 INFO @ Sun, 21 Jun 2020 19:16:59: 3000000 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 19:17:06: 4000000 INFO @ Sun, 21 Jun 2020 19:17:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.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 19:17:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:14: 5000000 INFO @ Sun, 21 Jun 2020 19:17:16: 1000000 INFO @ Sun, 21 Jun 2020 19:17:21: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:17:21: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:17:21: #1 total tags in treatment: 5905265 INFO @ Sun, 21 Jun 2020 19:17:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:21: #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 19:17:22: #1 tags after filtering in treatment: 5905097 INFO @ Sun, 21 Jun 2020 19:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:22: #2 number of paired peaks: 2791 INFO @ Sun, 21 Jun 2020 19:17:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:23: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:17:23: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 19:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.05_model.r INFO @ Sun, 21 Jun 2020 19:17:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:26: 2000000 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 19:17:35: 3000000 INFO @ Sun, 21 Jun 2020 19:17:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.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 19:17:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:44: 4000000 INFO @ Sun, 21 Jun 2020 19:17:45: 1000000 INFO @ Sun, 21 Jun 2020 19:17:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.05_summits.bed INFO @ Sun, 21 Jun 2020 19:17:46: Done! pass1 - making usageList (523 chroms): 2 millis pass2 - checking and writing primary data (3343 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:52: 2000000 INFO @ Sun, 21 Jun 2020 19:17:54: 5000000 INFO @ Sun, 21 Jun 2020 19:18:00: 3000000 INFO @ Sun, 21 Jun 2020 19:18:03: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:18:03: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:18:03: #1 total tags in treatment: 5905265 INFO @ Sun, 21 Jun 2020 19:18:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:03: #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 19:18:03: #1 tags after filtering in treatment: 5905097 INFO @ Sun, 21 Jun 2020 19:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:04: #2 number of paired peaks: 2791 INFO @ Sun, 21 Jun 2020 19:18:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:04: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:18:04: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 19:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.10_model.r INFO @ Sun, 21 Jun 2020 19:18:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:08: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:18:16: 5000000 INFO @ Sun, 21 Jun 2020 19:18:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:23: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:18:23: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:18:23: #1 total tags in treatment: 5905265 INFO @ Sun, 21 Jun 2020 19:18:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:23: #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 19:18:23: #1 tags after filtering in treatment: 5905097 INFO @ Sun, 21 Jun 2020 19:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:24: #2 number of paired peaks: 2791 INFO @ Sun, 21 Jun 2020 19:18:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:24: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:18:24: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 19:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.20_model.r INFO @ Sun, 21 Jun 2020 19:18:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.10_summits.bed INFO @ Sun, 21 Jun 2020 19:18:28: Done! pass1 - making usageList (446 chroms): 2 millis pass2 - checking and writing primary data (2429 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:18:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX273676/SRX273676.20_summits.bed INFO @ Sun, 21 Jun 2020 19:18:47: Done! pass1 - making usageList (345 chroms): 2 millis pass2 - checking and writing primary data (1752 records, 4 fields): 23 millis CompletedMACS2peakCalling