Job ID = 6626505 SRX = SRX5736483 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9412698 spots for SRR8956894/SRR8956894.sra Written 9412698 spots for SRR8956894/SRR8956894.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626668 ("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: 00:17:10 9412698 reads; of these: 9412698 (100.00%) were paired; of these: 2209989 (23.48%) aligned concordantly 0 times 6056100 (64.34%) aligned concordantly exactly 1 time 1146609 (12.18%) aligned concordantly >1 times ---- 2209989 pairs aligned concordantly 0 times; of these: 1127006 (51.00%) aligned discordantly 1 time ---- 1082983 pairs aligned 0 times concordantly or discordantly; of these: 2165966 mates make up the pairs; of these: 1364184 (62.98%) aligned 0 times 457080 (21.10%) aligned exactly 1 time 344702 (15.91%) aligned >1 times 92.75% overall alignment rate Time searching: 00:17:10 Overall time: 00:17:10 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] 700226 / 8290501 = 0.0845 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 07:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.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 07:33:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:33:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:33:48: 1000000 INFO @ Tue, 14 Jul 2020 07:33:55: 2000000 INFO @ Tue, 14 Jul 2020 07:34:02: 3000000 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 07:34:09: 4000000 INFO @ Tue, 14 Jul 2020 07:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.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 07:34:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:34:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:34:16: 5000000 INFO @ Tue, 14 Jul 2020 07:34:17: 1000000 INFO @ Tue, 14 Jul 2020 07:34:23: 6000000 INFO @ Tue, 14 Jul 2020 07:34:25: 2000000 INFO @ Tue, 14 Jul 2020 07:34:31: 7000000 INFO @ Tue, 14 Jul 2020 07:34:32: 3000000 INFO @ Tue, 14 Jul 2020 07:34:38: 8000000 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 07:34:40: 4000000 INFO @ Tue, 14 Jul 2020 07:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.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 07:34:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:34:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:34:46: 9000000 INFO @ Tue, 14 Jul 2020 07:34:47: 1000000 INFO @ Tue, 14 Jul 2020 07:34:47: 5000000 INFO @ Tue, 14 Jul 2020 07:34:53: 10000000 INFO @ Tue, 14 Jul 2020 07:34:54: 2000000 INFO @ Tue, 14 Jul 2020 07:34:55: 6000000 INFO @ Tue, 14 Jul 2020 07:35:00: 3000000 INFO @ Tue, 14 Jul 2020 07:35:01: 11000000 INFO @ Tue, 14 Jul 2020 07:35:02: 7000000 INFO @ Tue, 14 Jul 2020 07:35:07: 4000000 INFO @ Tue, 14 Jul 2020 07:35:08: 12000000 INFO @ Tue, 14 Jul 2020 07:35:10: 8000000 INFO @ Tue, 14 Jul 2020 07:35:14: 5000000 INFO @ Tue, 14 Jul 2020 07:35:15: 13000000 INFO @ Tue, 14 Jul 2020 07:35:19: 9000000 INFO @ Tue, 14 Jul 2020 07:35:21: 6000000 INFO @ Tue, 14 Jul 2020 07:35:23: 14000000 INFO @ Tue, 14 Jul 2020 07:35:27: 7000000 INFO @ Tue, 14 Jul 2020 07:35:29: 10000000 INFO @ Tue, 14 Jul 2020 07:35:30: 15000000 INFO @ Tue, 14 Jul 2020 07:35:34: 8000000 INFO @ Tue, 14 Jul 2020 07:35:37: 11000000 INFO @ Tue, 14 Jul 2020 07:35:38: 16000000 INFO @ Tue, 14 Jul 2020 07:35:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:35:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:35:38: #1 total tags in treatment: 6604680 INFO @ Tue, 14 Jul 2020 07:35:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:35:38: #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 07:35:38: #1 tags after filtering in treatment: 5791998 INFO @ Tue, 14 Jul 2020 07:35:38: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 14 Jul 2020 07:35:38: #1 finished! INFO @ Tue, 14 Jul 2020 07:35:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:35:39: #2 number of paired peaks: 2309 INFO @ Tue, 14 Jul 2020 07:35:39: start model_add_line... INFO @ Tue, 14 Jul 2020 07:35:39: start X-correlation... INFO @ Tue, 14 Jul 2020 07:35:39: end of X-cor INFO @ Tue, 14 Jul 2020 07:35:39: #2 finished! INFO @ Tue, 14 Jul 2020 07:35:39: #2 predicted fragment length is 284 bps INFO @ Tue, 14 Jul 2020 07:35:39: #2 alternative fragment length(s) may be 4,284 bps INFO @ Tue, 14 Jul 2020 07:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.05_model.r INFO @ Tue, 14 Jul 2020 07:35:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:35:41: 9000000 INFO @ Tue, 14 Jul 2020 07:35:45: 12000000 INFO @ Tue, 14 Jul 2020 07:35:49: 10000000 INFO @ Tue, 14 Jul 2020 07:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:35:54: 13000000 INFO @ Tue, 14 Jul 2020 07:35:56: 11000000 INFO @ Tue, 14 Jul 2020 07:36:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.05_summits.bed INFO @ Tue, 14 Jul 2020 07:36:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3339 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:02: 12000000 INFO @ Tue, 14 Jul 2020 07:36:04: 14000000 INFO @ Tue, 14 Jul 2020 07:36:09: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:36:13: 15000000 INFO @ Tue, 14 Jul 2020 07:36:17: 14000000 INFO @ Tue, 14 Jul 2020 07:36:22: 16000000 INFO @ Tue, 14 Jul 2020 07:36:23: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:36:23: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:36:23: #1 total tags in treatment: 6604680 INFO @ Tue, 14 Jul 2020 07:36:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:23: #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 07:36:23: #1 tags after filtering in treatment: 5791998 INFO @ Tue, 14 Jul 2020 07:36:23: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 14 Jul 2020 07:36:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:23: #2 number of paired peaks: 2309 INFO @ Tue, 14 Jul 2020 07:36:23: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:23: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:24: #2 predicted fragment length is 284 bps INFO @ Tue, 14 Jul 2020 07:36:24: #2 alternative fragment length(s) may be 4,284 bps INFO @ Tue, 14 Jul 2020 07:36:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.10_model.r INFO @ Tue, 14 Jul 2020 07:36:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:24: 15000000 INFO @ Tue, 14 Jul 2020 07:36:32: 16000000 INFO @ Tue, 14 Jul 2020 07:36:32: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:36:32: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:36:32: #1 total tags in treatment: 6604680 INFO @ Tue, 14 Jul 2020 07:36:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:32: #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 07:36:32: #1 tags after filtering in treatment: 5791998 INFO @ Tue, 14 Jul 2020 07:36:32: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 14 Jul 2020 07:36:32: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:33: #2 number of paired peaks: 2309 INFO @ Tue, 14 Jul 2020 07:36:33: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:33: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:33: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:33: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:33: #2 predicted fragment length is 284 bps INFO @ Tue, 14 Jul 2020 07:36:33: #2 alternative fragment length(s) may be 4,284 bps INFO @ Tue, 14 Jul 2020 07:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.20_model.r INFO @ Tue, 14 Jul 2020 07:36:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:36:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.10_summits.bed INFO @ Tue, 14 Jul 2020 07:36:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1242 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736483/SRX5736483.20_summits.bed INFO @ Tue, 14 Jul 2020 07:36:54: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 15 millis CompletedMACS2peakCalling