Job ID = 6457096 SRX = SRX4375856 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:27:54 prefetch.2.10.7: 1) Downloading 'SRR7506510'... 2020-06-21T11:27:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:30:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:30:30 prefetch.2.10.7: 'SRR7506510' is valid 2020-06-21T11:30:30 prefetch.2.10.7: 1) 'SRR7506510' was downloaded successfully Read 13485141 spots for SRR7506510/SRR7506510.sra Written 13485141 spots for SRR7506510/SRR7506510.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: 00:03:09 13485141 reads; of these: 13485141 (100.00%) were unpaired; of these: 2080360 (15.43%) aligned 0 times 9443716 (70.03%) aligned exactly 1 time 1961065 (14.54%) aligned >1 times 84.57% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4028439 / 11404781 = 0.3532 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 20:37:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.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 20:37:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:23: 1000000 INFO @ Sun, 21 Jun 2020 20:37:29: 2000000 INFO @ Sun, 21 Jun 2020 20:37:34: 3000000 INFO @ Sun, 21 Jun 2020 20:37:40: 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 20:37:46: 5000000 INFO @ Sun, 21 Jun 2020 20:37:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.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 20:37:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:52: 6000000 INFO @ Sun, 21 Jun 2020 20:37:54: 1000000 INFO @ Sun, 21 Jun 2020 20:37:58: 7000000 INFO @ Sun, 21 Jun 2020 20:38:00: 2000000 INFO @ Sun, 21 Jun 2020 20:38:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:38:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:38:01: #1 total tags in treatment: 7376342 INFO @ Sun, 21 Jun 2020 20:38:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:01: #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 20:38:01: #1 tags after filtering in treatment: 7376107 INFO @ Sun, 21 Jun 2020 20:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:02: #2 number of paired peaks: 8582 INFO @ Sun, 21 Jun 2020 20:38:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:02: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 20:38:02: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 20:38:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.05_model.r INFO @ Sun, 21 Jun 2020 20:38:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:06: 3000000 INFO @ Sun, 21 Jun 2020 20:38:12: 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 20:38:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.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 20:38:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:18: 5000000 INFO @ Sun, 21 Jun 2020 20:38:25: 1000000 INFO @ Sun, 21 Jun 2020 20:38:25: 6000000 INFO @ Sun, 21 Jun 2020 20:38:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:32: 2000000 INFO @ Sun, 21 Jun 2020 20:38:32: 7000000 INFO @ Sun, 21 Jun 2020 20:38:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:38:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:38:35: #1 total tags in treatment: 7376342 INFO @ Sun, 21 Jun 2020 20:38:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:35: #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 20:38:35: #1 tags after filtering in treatment: 7376107 INFO @ Sun, 21 Jun 2020 20:38:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:37: #2 number of paired peaks: 8582 INFO @ Sun, 21 Jun 2020 20:38:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:37: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 20:38:37: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 20:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.10_model.r INFO @ Sun, 21 Jun 2020 20:38:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.05_summits.bed INFO @ Sun, 21 Jun 2020 20:38:37: Done! pass1 - making usageList (153 chroms): 2 millis pass2 - checking and writing primary data (8463 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:39: 3000000 INFO @ Sun, 21 Jun 2020 20:38:47: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:38:53: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:39:00: 6000000 INFO @ Sun, 21 Jun 2020 20:39:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:07: 7000000 INFO @ Sun, 21 Jun 2020 20:39:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:39:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:39:09: #1 total tags in treatment: 7376342 INFO @ Sun, 21 Jun 2020 20:39:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:09: #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 20:39:10: #1 tags after filtering in treatment: 7376107 INFO @ Sun, 21 Jun 2020 20:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:11: #2 number of paired peaks: 8582 INFO @ Sun, 21 Jun 2020 20:39:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:11: #2 predicted fragment length is 200 bps INFO @ Sun, 21 Jun 2020 20:39:11: #2 alternative fragment length(s) may be 200 bps INFO @ Sun, 21 Jun 2020 20:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.20_model.r INFO @ Sun, 21 Jun 2020 20:39:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.10_summits.bed INFO @ Sun, 21 Jun 2020 20:39:11: Done! pass1 - making usageList (124 chroms): 1 millis pass2 - checking and writing primary data (6810 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:39:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375856/SRX4375856.20_summits.bed INFO @ Sun, 21 Jun 2020 20:39:46: Done! pass1 - making usageList (94 chroms): 2 millis pass2 - checking and writing primary data (5206 records, 4 fields): 9 millis CompletedMACS2peakCalling