Job ID = 6455914 SRX = SRX3068954 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:21 prefetch.2.10.7: 1) Downloading 'SRR5907430'... 2020-06-21T10:24:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:02 prefetch.2.10.7: 1) 'SRR5907430' was downloaded successfully Read 21947870 spots for SRR5907430/SRR5907430.sra Written 21947870 spots for SRR5907430/SRR5907430.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: 00:03:13 21947870 reads; of these: 21947870 (100.00%) were unpaired; of these: 12560097 (57.23%) aligned 0 times 7736073 (35.25%) aligned exactly 1 time 1651700 (7.53%) aligned >1 times 42.77% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 3044618 / 9387773 = 0.3243 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 19:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.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 19:34:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:04: 1000000 INFO @ Sun, 21 Jun 2020 19:35:09: 2000000 INFO @ Sun, 21 Jun 2020 19:35:14: 3000000 INFO @ Sun, 21 Jun 2020 19:35:20: 4000000 INFO @ Sun, 21 Jun 2020 19:35:25: 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 19:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.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 19:35:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:31: 6000000 INFO @ Sun, 21 Jun 2020 19:35:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:35:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:35:33: #1 total tags in treatment: 6343155 INFO @ Sun, 21 Jun 2020 19:35:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:33: #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 19:35:34: #1 tags after filtering in treatment: 6343132 INFO @ Sun, 21 Jun 2020 19:35:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:34: #2 number of paired peaks: 1284 INFO @ Sun, 21 Jun 2020 19:35:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:34: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:35:34: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 19:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.05_model.r INFO @ Sun, 21 Jun 2020 19:35:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:36: 1000000 INFO @ Sun, 21 Jun 2020 19:35:43: 2000000 INFO @ Sun, 21 Jun 2020 19:35:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:49: 3000000 INFO @ Sun, 21 Jun 2020 19:35:55: 4000000 INFO @ Sun, 21 Jun 2020 19:35:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:56: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (5490 records, 4 fields): 18 millis CompletedMACS2peakCalling 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 19:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.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 19:35:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:02: 5000000 INFO @ Sun, 21 Jun 2020 19:36:04: 1000000 INFO @ Sun, 21 Jun 2020 19:36:10: 6000000 INFO @ Sun, 21 Jun 2020 19:36:11: 2000000 INFO @ Sun, 21 Jun 2020 19:36:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:12: #1 total tags in treatment: 6343155 INFO @ Sun, 21 Jun 2020 19:36:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:12: #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 19:36:13: #1 tags after filtering in treatment: 6343132 INFO @ Sun, 21 Jun 2020 19:36:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:13: #2 number of paired peaks: 1284 INFO @ Sun, 21 Jun 2020 19:36:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:13: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:36:13: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 19:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.10_model.r INFO @ Sun, 21 Jun 2020 19:36:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:17: 3000000 INFO @ Sun, 21 Jun 2020 19:36:22: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:29: 5000000 INFO @ Sun, 21 Jun 2020 19:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:34: Done! INFO @ Sun, 21 Jun 2020 19:36:35: 6000000 pass1 - making usageList (421 chroms): 2 millis pass2 - checking and writing primary data (2966 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:37: #1 total tags in treatment: 6343155 INFO @ Sun, 21 Jun 2020 19:36:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:37: #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 19:36:37: #1 tags after filtering in treatment: 6343132 INFO @ Sun, 21 Jun 2020 19:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:38: #2 number of paired peaks: 1284 INFO @ Sun, 21 Jun 2020 19:36:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:38: #2 predicted fragment length is 127 bps INFO @ Sun, 21 Jun 2020 19:36:38: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 21 Jun 2020 19:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.20_model.r INFO @ Sun, 21 Jun 2020 19:36:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068954/SRX3068954.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:00: Done! pass1 - making usageList (278 chroms): 1 millis pass2 - checking and writing primary data (1190 records, 4 fields): 9 millis CompletedMACS2peakCalling