Job ID = 6454905 SRX = SRX2592490 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:25 prefetch.2.10.7: 1) Downloading 'SRR5289767'... 2020-06-21T09:58:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:27 prefetch.2.10.7: 'SRR5289767' is valid 2020-06-21T09:59:27 prefetch.2.10.7: 1) 'SRR5289767' was downloaded successfully Read 7758661 spots for SRR5289767/SRR5289767.sra Written 7758661 spots for SRR5289767/SRR5289767.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: 00:01:27 7758661 reads; of these: 7758661 (100.00%) were unpaired; of these: 3629198 (46.78%) aligned 0 times 3286711 (42.36%) aligned exactly 1 time 842752 (10.86%) aligned >1 times 53.22% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 530845 / 4129463 = 0.1286 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 19:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.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 19:03:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:27: 1000000 INFO @ Sun, 21 Jun 2020 19:03:37: 2000000 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 19:03:47: 3000000 INFO @ Sun, 21 Jun 2020 19:03:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.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 19:03:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:03:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:03:53: #1 total tags in treatment: 3598618 INFO @ Sun, 21 Jun 2020 19:03:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:53: #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 19:03:53: #1 tags after filtering in treatment: 3598316 INFO @ Sun, 21 Jun 2020 19:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:54: #2 number of paired peaks: 3043 INFO @ Sun, 21 Jun 2020 19:03:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:54: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:03:54: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.05_model.r INFO @ Sun, 21 Jun 2020 19:03:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:57: 1000000 INFO @ Sun, 21 Jun 2020 19:04:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:07: 2000000 INFO @ Sun, 21 Jun 2020 19:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:08: Done! pass1 - making usageList (214 chroms): 2 millis pass2 - checking and writing primary data (5243 records, 4 fields): 19 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 19:04:17: 3000000 INFO @ Sun, 21 Jun 2020 19:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.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 19:04:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:04:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:04:23: #1 total tags in treatment: 3598618 INFO @ Sun, 21 Jun 2020 19:04:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:23: #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 19:04:24: #1 tags after filtering in treatment: 3598316 INFO @ Sun, 21 Jun 2020 19:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:24: #2 number of paired peaks: 3043 INFO @ Sun, 21 Jun 2020 19:04:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:24: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:04:24: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.10_model.r INFO @ Sun, 21 Jun 2020 19:04:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:28: 1000000 INFO @ Sun, 21 Jun 2020 19:04:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:37: 2000000 INFO @ Sun, 21 Jun 2020 19:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.10_summits.bed INFO @ Sun, 21 Jun 2020 19:04:38: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (2608 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:48: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:04:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:04:54: #1 total tags in treatment: 3598618 INFO @ Sun, 21 Jun 2020 19:04:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:54: #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 19:04:54: #1 tags after filtering in treatment: 3598316 INFO @ Sun, 21 Jun 2020 19:04:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:55: #2 number of paired peaks: 3043 INFO @ Sun, 21 Jun 2020 19:04:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:55: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:04:55: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 19:04:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.20_model.r INFO @ Sun, 21 Jun 2020 19:04:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592490/SRX2592490.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:09: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (1012 records, 4 fields): 5 millis CompletedMACS2peakCalling