Job ID = 6456891 SRX = SRX4053301 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:34:55 prefetch.2.10.7: 1) Downloading 'SRR7132412'... 2020-06-21T11:34:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:12 prefetch.2.10.7: 'SRR7132412' is valid 2020-06-21T11:37:12 prefetch.2.10.7: 1) 'SRR7132412' was downloaded successfully 2020-06-21T11:37:12 prefetch.2.10.7: 'SRR7132412' has 0 unresolved dependencies Read 15237629 spots for SRR7132412/SRR7132412.sra Written 15237629 spots for SRR7132412/SRR7132412.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: 00:04:03 15237629 reads; of these: 15237629 (100.00%) were unpaired; of these: 1927398 (12.65%) aligned 0 times 10654217 (69.92%) aligned exactly 1 time 2656014 (17.43%) aligned >1 times 87.35% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 4290389 / 13310231 = 0.3223 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 20:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.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 20:45:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:15: 1000000 INFO @ Sun, 21 Jun 2020 20:45:20: 2000000 INFO @ Sun, 21 Jun 2020 20:45:25: 3000000 INFO @ Sun, 21 Jun 2020 20:45:30: 4000000 INFO @ Sun, 21 Jun 2020 20:45:35: 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 20:45:40: 6000000 INFO @ Sun, 21 Jun 2020 20:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.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 20:45:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:45: 7000000 INFO @ Sun, 21 Jun 2020 20:45:45: 1000000 INFO @ Sun, 21 Jun 2020 20:45:50: 2000000 INFO @ Sun, 21 Jun 2020 20:45:50: 8000000 INFO @ Sun, 21 Jun 2020 20:45:55: 3000000 INFO @ Sun, 21 Jun 2020 20:45:56: 9000000 INFO @ Sun, 21 Jun 2020 20:45:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:45:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:45:56: #1 total tags in treatment: 9019842 INFO @ Sun, 21 Jun 2020 20:45:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:56: #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 20:45:56: #1 tags after filtering in treatment: 9019826 INFO @ Sun, 21 Jun 2020 20:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:57: #2 number of paired peaks: 6113 INFO @ Sun, 21 Jun 2020 20:45:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:58: #2 predicted fragment length is 220 bps INFO @ Sun, 21 Jun 2020 20:45:58: #2 alternative fragment length(s) may be 2,220 bps INFO @ Sun, 21 Jun 2020 20:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.05_model.r INFO @ Sun, 21 Jun 2020 20:45:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:46:00: 4000000 INFO @ Sun, 21 Jun 2020 20:46:05: 5000000 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 20:46:10: 6000000 INFO @ Sun, 21 Jun 2020 20:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.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 20:46:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:15: 7000000 INFO @ Sun, 21 Jun 2020 20:46:16: 1000000 INFO @ Sun, 21 Jun 2020 20:46:20: 8000000 INFO @ Sun, 21 Jun 2020 20:46:22: 2000000 INFO @ Sun, 21 Jun 2020 20:46:25: 9000000 INFO @ Sun, 21 Jun 2020 20:46:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:46:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:46:26: #1 total tags in treatment: 9019842 INFO @ Sun, 21 Jun 2020 20:46:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:26: #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 20:46:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:46:26: #1 tags after filtering in treatment: 9019826 INFO @ Sun, 21 Jun 2020 20:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:46:27: #2 number of paired peaks: 6113 INFO @ Sun, 21 Jun 2020 20:46:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:46:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:46:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:46:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:46:27: #2 predicted fragment length is 220 bps INFO @ Sun, 21 Jun 2020 20:46:27: #2 alternative fragment length(s) may be 2,220 bps INFO @ Sun, 21 Jun 2020 20:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.10_model.r INFO @ Sun, 21 Jun 2020 20:46:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:46:28: 3000000 INFO @ Sun, 21 Jun 2020 20:46:34: 4000000 INFO @ Sun, 21 Jun 2020 20:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.05_summits.bed INFO @ Sun, 21 Jun 2020 20:46:37: Done! pass1 - making usageList (573 chroms): 1 millis pass2 - checking and writing primary data (2333 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:40: 5000000 INFO @ Sun, 21 Jun 2020 20:46:46: 6000000 INFO @ Sun, 21 Jun 2020 20:46:51: 7000000 INFO @ Sun, 21 Jun 2020 20:46:55: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:46:57: 8000000 INFO @ Sun, 21 Jun 2020 20:47:03: 9000000 INFO @ Sun, 21 Jun 2020 20:47:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:47:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:47:04: #1 total tags in treatment: 9019842 INFO @ Sun, 21 Jun 2020 20:47:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:04: #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 20:47:04: #1 tags after filtering in treatment: 9019826 INFO @ Sun, 21 Jun 2020 20:47:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:05: #2 number of paired peaks: 6113 INFO @ Sun, 21 Jun 2020 20:47:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:05: #2 predicted fragment length is 220 bps INFO @ Sun, 21 Jun 2020 20:47:05: #2 alternative fragment length(s) may be 2,220 bps INFO @ Sun, 21 Jun 2020 20:47:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.20_model.r INFO @ Sun, 21 Jun 2020 20:47:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.10_summits.bed INFO @ Sun, 21 Jun 2020 20:47:06: Done! pass1 - making usageList (391 chroms): 1 millis pass2 - checking and writing primary data (1120 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:47:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053301/SRX4053301.20_summits.bed INFO @ Sun, 21 Jun 2020 20:47:43: Done! pass1 - making usageList (147 chroms): 1 millis pass2 - checking and writing primary data (334 records, 4 fields): 5 millis CompletedMACS2peakCalling