Job ID = 6455925 SRX = SRX3068964 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:34:11 prefetch.2.10.7: 1) Downloading 'SRR5907440'... 2020-06-21T10:34:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:35:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:35:54 prefetch.2.10.7: 'SRR5907440' is valid 2020-06-21T10:35:54 prefetch.2.10.7: 1) 'SRR5907440' was downloaded successfully Read 10743895 spots for SRR5907440/SRR5907440.sra Written 10743895 spots for SRR5907440/SRR5907440.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: 00:02:04 10743895 reads; of these: 10743895 (100.00%) were unpaired; of these: 1870816 (17.41%) aligned 0 times 7859174 (73.15%) aligned exactly 1 time 1013905 (9.44%) aligned >1 times 82.59% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 2870898 / 8873079 = 0.3236 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 19:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.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 19:41:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:44: 1000000 INFO @ Sun, 21 Jun 2020 19:41:50: 2000000 INFO @ Sun, 21 Jun 2020 19:41:56: 3000000 INFO @ Sun, 21 Jun 2020 19:42:02: 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 19:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.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 19:42:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:09: 5000000 INFO @ Sun, 21 Jun 2020 19:42:15: 1000000 INFO @ Sun, 21 Jun 2020 19:42:16: 6000000 INFO @ Sun, 21 Jun 2020 19:42:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:42:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:42:16: #1 total tags in treatment: 6002181 INFO @ Sun, 21 Jun 2020 19:42:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:16: #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 19:42:17: #1 tags after filtering in treatment: 6002051 INFO @ Sun, 21 Jun 2020 19:42:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:18: #2 number of paired peaks: 2991 INFO @ Sun, 21 Jun 2020 19:42:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:18: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:42:18: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:42:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.05_model.r INFO @ Sun, 21 Jun 2020 19:42:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:21: 2000000 INFO @ Sun, 21 Jun 2020 19:42:27: 3000000 INFO @ Sun, 21 Jun 2020 19:42:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:34: 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 19:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.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 19:42:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.05_summits.bed INFO @ Sun, 21 Jun 2020 19:42:40: Done! pass1 - making usageList (411 chroms): 3 millis pass2 - checking and writing primary data (9653 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:42:41: 5000000 INFO @ Sun, 21 Jun 2020 19:42:45: 1000000 INFO @ Sun, 21 Jun 2020 19:42:48: 6000000 INFO @ Sun, 21 Jun 2020 19:42:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:42:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:42:48: #1 total tags in treatment: 6002181 INFO @ Sun, 21 Jun 2020 19:42:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:48: #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 19:42:49: #1 tags after filtering in treatment: 6002051 INFO @ Sun, 21 Jun 2020 19:42:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:50: #2 number of paired peaks: 2991 INFO @ Sun, 21 Jun 2020 19:42:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:50: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:42:50: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:42:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.10_model.r INFO @ Sun, 21 Jun 2020 19:42:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:51: 2000000 INFO @ Sun, 21 Jun 2020 19:42:58: 3000000 INFO @ Sun, 21 Jun 2020 19:43:04: 4000000 INFO @ Sun, 21 Jun 2020 19:43:04: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:43:12: 5000000 INFO @ Sun, 21 Jun 2020 19:43:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.10_summits.bed INFO @ Sun, 21 Jun 2020 19:43:12: Done! pass1 - making usageList (323 chroms): 2 millis pass2 - checking and writing primary data (6240 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:19: 6000000 INFO @ Sun, 21 Jun 2020 19:43:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:19: #1 total tags in treatment: 6002181 INFO @ Sun, 21 Jun 2020 19:43:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:19: #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 19:43:20: #1 tags after filtering in treatment: 6002051 INFO @ Sun, 21 Jun 2020 19:43:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:20: #2 number of paired peaks: 2991 INFO @ Sun, 21 Jun 2020 19:43:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:20: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:43:20: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.20_model.r INFO @ Sun, 21 Jun 2020 19:43:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:43:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068964/SRX3068964.20_summits.bed INFO @ Sun, 21 Jun 2020 19:43:42: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (2705 records, 4 fields): 11 millis CompletedMACS2peakCalling