Job ID = 6454910 SRX = SRX2592495 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:25 prefetch.2.10.7: 1) Downloading 'SRR5289772'... 2020-06-21T09:37:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:37:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:37:56 prefetch.2.10.7: 'SRR5289772' is valid 2020-06-21T09:37:56 prefetch.2.10.7: 1) 'SRR5289772' was downloaded successfully Read 2031880 spots for SRR5289772/SRR5289772.sra Written 2031880 spots for SRR5289772/SRR5289772.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: 00:00:23 2031880 reads; of these: 2031880 (100.00%) were unpaired; of these: 779037 (38.34%) aligned 0 times 1105432 (54.40%) aligned exactly 1 time 147411 (7.25%) aligned >1 times 61.66% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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] 66895 / 1252843 = 0.0534 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 18:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.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 18:39:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:26: 1000000 INFO @ Sun, 21 Jun 2020 18:39:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:28: #1 total tags in treatment: 1185948 INFO @ Sun, 21 Jun 2020 18:39:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:28: #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 18:39:28: #1 tags after filtering in treatment: 1185243 INFO @ Sun, 21 Jun 2020 18:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:29: #2 number of paired peaks: 7499 INFO @ Sun, 21 Jun 2020 18:39:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:29: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 18:39:29: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 18:39:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.05_model.r INFO @ Sun, 21 Jun 2020 18:39:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:34: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (4322 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 18:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.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 18:39:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:56: 1000000 INFO @ Sun, 21 Jun 2020 18:39:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:58: #1 total tags in treatment: 1185948 INFO @ Sun, 21 Jun 2020 18:39:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:58: #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 18:39:59: #1 tags after filtering in treatment: 1185243 INFO @ Sun, 21 Jun 2020 18:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:59: #2 number of paired peaks: 7499 INFO @ Sun, 21 Jun 2020 18:39:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:59: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 18:39:59: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 18:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.10_model.r INFO @ Sun, 21 Jun 2020 18:39:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:04: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (2450 records, 4 fields): 5 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 18:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.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 18:40:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:20: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:26: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:28: #1 total tags in treatment: 1185948 INFO @ Sun, 21 Jun 2020 18:40:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:28: #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 18:40:29: #1 tags after filtering in treatment: 1185243 INFO @ Sun, 21 Jun 2020 18:40:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:29: #2 number of paired peaks: 7499 INFO @ Sun, 21 Jun 2020 18:40:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:29: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 18:40:29: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 18:40:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.20_model.r INFO @ Sun, 21 Jun 2020 18:40:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592495/SRX2592495.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:34: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (832 records, 4 fields): 3 millis CompletedMACS2peakCalling