Job ID = 6626504 SRX = SRX5736482 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8434103 spots for SRR8956893/SRR8956893.sra Written 8434103 spots for SRR8956893/SRR8956893.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626651 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:04 8434103 reads; of these: 8434103 (100.00%) were paired; of these: 2706601 (32.09%) aligned concordantly 0 times 4539500 (53.82%) aligned concordantly exactly 1 time 1188002 (14.09%) aligned concordantly >1 times ---- 2706601 pairs aligned concordantly 0 times; of these: 796660 (29.43%) aligned discordantly 1 time ---- 1909941 pairs aligned 0 times concordantly or discordantly; of these: 3819882 mates make up the pairs; of these: 3080703 (80.65%) aligned 0 times 378474 (9.91%) aligned exactly 1 time 360705 (9.44%) aligned >1 times 81.74% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 668650 / 6491343 = 0.1030 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 @ Tue, 14 Jul 2020 07:28:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.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 @ Tue, 14 Jul 2020 07:28:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:26: 1000000 INFO @ Tue, 14 Jul 2020 07:28:32: 2000000 INFO @ Tue, 14 Jul 2020 07:28:38: 3000000 INFO @ Tue, 14 Jul 2020 07:28:44: 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 @ Tue, 14 Jul 2020 07:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.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 @ Tue, 14 Jul 2020 07:28:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:51: 5000000 INFO @ Tue, 14 Jul 2020 07:28:56: 1000000 INFO @ Tue, 14 Jul 2020 07:28:58: 6000000 INFO @ Tue, 14 Jul 2020 07:29:03: 2000000 INFO @ Tue, 14 Jul 2020 07:29:06: 7000000 INFO @ Tue, 14 Jul 2020 07:29:09: 3000000 INFO @ Tue, 14 Jul 2020 07:29:14: 8000000 INFO @ Tue, 14 Jul 2020 07:29:16: 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 @ Tue, 14 Jul 2020 07:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.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 @ Tue, 14 Jul 2020 07:29:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:21: 9000000 INFO @ Tue, 14 Jul 2020 07:29:22: 5000000 INFO @ Tue, 14 Jul 2020 07:29:26: 1000000 INFO @ Tue, 14 Jul 2020 07:29:29: 10000000 INFO @ Tue, 14 Jul 2020 07:29:29: 6000000 INFO @ Tue, 14 Jul 2020 07:29:33: 2000000 INFO @ Tue, 14 Jul 2020 07:29:36: 7000000 INFO @ Tue, 14 Jul 2020 07:29:36: 11000000 INFO @ Tue, 14 Jul 2020 07:29:40: 3000000 INFO @ Tue, 14 Jul 2020 07:29:42: 8000000 INFO @ Tue, 14 Jul 2020 07:29:43: 12000000 INFO @ Tue, 14 Jul 2020 07:29:46: 4000000 INFO @ Tue, 14 Jul 2020 07:29:46: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:29:46: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:29:46: #1 total tags in treatment: 5139760 INFO @ Tue, 14 Jul 2020 07:29:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:29:47: #1 tags after filtering in treatment: 4617942 INFO @ Tue, 14 Jul 2020 07:29:47: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:29:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:47: #2 number of paired peaks: 1876 INFO @ Tue, 14 Jul 2020 07:29:47: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:47: #2 predicted fragment length is 205 bps INFO @ Tue, 14 Jul 2020 07:29:47: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 14 Jul 2020 07:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.05_model.r INFO @ Tue, 14 Jul 2020 07:29:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:49: 9000000 INFO @ Tue, 14 Jul 2020 07:29:52: 5000000 INFO @ Tue, 14 Jul 2020 07:29:55: 10000000 INFO @ Tue, 14 Jul 2020 07:29:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:58: 6000000 INFO @ Tue, 14 Jul 2020 07:30:01: 11000000 INFO @ Tue, 14 Jul 2020 07:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.05_summits.bed INFO @ Tue, 14 Jul 2020 07:30:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3472 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:30:04: 7000000 INFO @ Tue, 14 Jul 2020 07:30:07: 12000000 INFO @ Tue, 14 Jul 2020 07:30:09: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:30:09: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:30:09: #1 total tags in treatment: 5139760 INFO @ Tue, 14 Jul 2020 07:30:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:30:09: #1 tags after filtering in treatment: 4617942 INFO @ Tue, 14 Jul 2020 07:30:09: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:30:09: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:10: #2 number of paired peaks: 1876 INFO @ Tue, 14 Jul 2020 07:30:10: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:10: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:10: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:10: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:10: #2 predicted fragment length is 205 bps INFO @ Tue, 14 Jul 2020 07:30:10: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 14 Jul 2020 07:30:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.10_model.r INFO @ Tue, 14 Jul 2020 07:30:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:30:10: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:30:16: 9000000 INFO @ Tue, 14 Jul 2020 07:30:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:22: 10000000 INFO @ Tue, 14 Jul 2020 07:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.10_summits.bed INFO @ Tue, 14 Jul 2020 07:30:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1190 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:30:27: 11000000 INFO @ Tue, 14 Jul 2020 07:30:33: 12000000 INFO @ Tue, 14 Jul 2020 07:30:35: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:30:35: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:30:35: #1 total tags in treatment: 5139760 INFO @ Tue, 14 Jul 2020 07:30:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:30:35: #1 tags after filtering in treatment: 4617942 INFO @ Tue, 14 Jul 2020 07:30:35: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:30:35: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:36: #2 number of paired peaks: 1876 INFO @ Tue, 14 Jul 2020 07:30:36: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:36: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:36: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:36: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:36: #2 predicted fragment length is 205 bps INFO @ Tue, 14 Jul 2020 07:30:36: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 14 Jul 2020 07:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.20_model.r INFO @ Tue, 14 Jul 2020 07:30:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:30:46: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736482/SRX5736482.20_summits.bed INFO @ Tue, 14 Jul 2020 07:30:51: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 27 millis CompletedMACS2peakCalling