Job ID = 16439610 SRX = SRX9518343 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20802512 spots for SRR13070826/SRR13070826.sra Written 20802512 spots for SRR13070826/SRR13070826.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440024 ("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: 00:53:31 20802512 reads; of these: 20802512 (100.00%) were paired; of these: 1813076 (8.72%) aligned concordantly 0 times 15111958 (72.64%) aligned concordantly exactly 1 time 3877478 (18.64%) aligned concordantly >1 times ---- 1813076 pairs aligned concordantly 0 times; of these: 185452 (10.23%) aligned discordantly 1 time ---- 1627624 pairs aligned 0 times concordantly or discordantly; of these: 3255248 mates make up the pairs; of these: 2479577 (76.17%) aligned 0 times 454496 (13.96%) aligned exactly 1 time 321175 (9.87%) aligned >1 times 94.04% overall alignment rate Time searching: 00:53:31 Overall time: 00:53:31 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 16 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] 4062949 / 19132676 = 0.2124 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.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, 02 Aug 2022 16:49:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:49:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:50:05: 1000000 INFO @ Tue, 02 Aug 2022 16:50:13: 2000000 INFO @ Tue, 02 Aug 2022 16:50:20: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.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, 02 Aug 2022 16:50:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:50:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:50:28: 4000000 INFO @ Tue, 02 Aug 2022 16:50:34: 1000000 INFO @ Tue, 02 Aug 2022 16:50:35: 5000000 INFO @ Tue, 02 Aug 2022 16:50:41: 2000000 INFO @ Tue, 02 Aug 2022 16:50:43: 6000000 INFO @ Tue, 02 Aug 2022 16:50:47: 3000000 INFO @ Tue, 02 Aug 2022 16:50:50: 7000000 INFO @ Tue, 02 Aug 2022 16:50:54: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:50:58: 8000000 INFO @ Tue, 02 Aug 2022 16:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.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, 02 Aug 2022 16:50:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:50:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:51:03: 5000000 INFO @ Tue, 02 Aug 2022 16:51:04: 1000000 INFO @ Tue, 02 Aug 2022 16:51:05: 9000000 INFO @ Tue, 02 Aug 2022 16:51:11: 6000000 INFO @ Tue, 02 Aug 2022 16:51:11: 2000000 INFO @ Tue, 02 Aug 2022 16:51:13: 10000000 INFO @ Tue, 02 Aug 2022 16:51:19: 7000000 INFO @ Tue, 02 Aug 2022 16:51:19: 3000000 INFO @ Tue, 02 Aug 2022 16:51:20: 11000000 INFO @ Tue, 02 Aug 2022 16:51:27: 8000000 INFO @ Tue, 02 Aug 2022 16:51:27: 4000000 INFO @ Tue, 02 Aug 2022 16:51:28: 12000000 INFO @ Tue, 02 Aug 2022 16:51:34: 9000000 INFO @ Tue, 02 Aug 2022 16:51:35: 13000000 INFO @ Tue, 02 Aug 2022 16:51:35: 5000000 INFO @ Tue, 02 Aug 2022 16:51:42: 14000000 INFO @ Tue, 02 Aug 2022 16:51:42: 10000000 INFO @ Tue, 02 Aug 2022 16:51:43: 6000000 INFO @ Tue, 02 Aug 2022 16:51:49: 15000000 INFO @ Tue, 02 Aug 2022 16:51:50: 11000000 INFO @ Tue, 02 Aug 2022 16:51:50: 7000000 INFO @ Tue, 02 Aug 2022 16:51:56: 16000000 INFO @ Tue, 02 Aug 2022 16:51:57: 12000000 INFO @ Tue, 02 Aug 2022 16:51:58: 8000000 INFO @ Tue, 02 Aug 2022 16:52:03: 17000000 INFO @ Tue, 02 Aug 2022 16:52:04: 13000000 INFO @ Tue, 02 Aug 2022 16:52:06: 9000000 INFO @ Tue, 02 Aug 2022 16:52:10: 18000000 INFO @ Tue, 02 Aug 2022 16:52:12: 14000000 INFO @ Tue, 02 Aug 2022 16:52:14: 10000000 INFO @ Tue, 02 Aug 2022 16:52:17: 19000000 INFO @ Tue, 02 Aug 2022 16:52:20: 15000000 INFO @ Tue, 02 Aug 2022 16:52:21: 11000000 INFO @ Tue, 02 Aug 2022 16:52:24: 20000000 INFO @ Tue, 02 Aug 2022 16:52:28: 16000000 INFO @ Tue, 02 Aug 2022 16:52:28: 12000000 INFO @ Tue, 02 Aug 2022 16:52:31: 21000000 INFO @ Tue, 02 Aug 2022 16:52:36: 17000000 INFO @ Tue, 02 Aug 2022 16:52:36: 13000000 INFO @ Tue, 02 Aug 2022 16:52:38: 22000000 INFO @ Tue, 02 Aug 2022 16:52:43: 18000000 INFO @ Tue, 02 Aug 2022 16:52:43: 14000000 INFO @ Tue, 02 Aug 2022 16:52:45: 23000000 INFO @ Tue, 02 Aug 2022 16:52:51: 19000000 INFO @ Tue, 02 Aug 2022 16:52:51: 15000000 INFO @ Tue, 02 Aug 2022 16:52:52: 24000000 INFO @ Tue, 02 Aug 2022 16:52:58: 20000000 INFO @ Tue, 02 Aug 2022 16:52:59: 16000000 INFO @ Tue, 02 Aug 2022 16:53:00: 25000000 INFO @ Tue, 02 Aug 2022 16:53:06: 21000000 INFO @ Tue, 02 Aug 2022 16:53:06: 17000000 INFO @ Tue, 02 Aug 2022 16:53:07: 26000000 INFO @ Tue, 02 Aug 2022 16:53:14: 22000000 INFO @ Tue, 02 Aug 2022 16:53:14: 18000000 INFO @ Tue, 02 Aug 2022 16:53:15: 27000000 INFO @ Tue, 02 Aug 2022 16:53:21: 23000000 INFO @ Tue, 02 Aug 2022 16:53:22: 19000000 INFO @ Tue, 02 Aug 2022 16:53:22: 28000000 INFO @ Tue, 02 Aug 2022 16:53:29: 29000000 INFO @ Tue, 02 Aug 2022 16:53:29: 24000000 INFO @ Tue, 02 Aug 2022 16:53:29: 20000000 INFO @ Tue, 02 Aug 2022 16:53:36: 30000000 INFO @ Tue, 02 Aug 2022 16:53:37: 25000000 INFO @ Tue, 02 Aug 2022 16:53:37: 21000000 INFO @ Tue, 02 Aug 2022 16:53:43: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:53:43: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:53:43: #1 total tags in treatment: 14942205 INFO @ Tue, 02 Aug 2022 16:53:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:53:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:53:43: #1 tags after filtering in treatment: 13796344 INFO @ Tue, 02 Aug 2022 16:53:43: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 16:53:43: #1 finished! INFO @ Tue, 02 Aug 2022 16:53:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:53:45: #2 number of paired peaks: 1983 INFO @ Tue, 02 Aug 2022 16:53:45: start model_add_line... INFO @ Tue, 02 Aug 2022 16:53:45: 26000000 INFO @ Tue, 02 Aug 2022 16:53:45: start X-correlation... INFO @ Tue, 02 Aug 2022 16:53:45: 22000000 INFO @ Tue, 02 Aug 2022 16:53:45: end of X-cor INFO @ Tue, 02 Aug 2022 16:53:45: #2 finished! INFO @ Tue, 02 Aug 2022 16:53:45: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 16:53:45: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 02 Aug 2022 16:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.05_model.r INFO @ Tue, 02 Aug 2022 16:53:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:53:52: 23000000 INFO @ Tue, 02 Aug 2022 16:53:52: 27000000 INFO @ Tue, 02 Aug 2022 16:54:00: 28000000 INFO @ Tue, 02 Aug 2022 16:54:00: 24000000 INFO @ Tue, 02 Aug 2022 16:54:07: 29000000 INFO @ Tue, 02 Aug 2022 16:54:08: 25000000 INFO @ Tue, 02 Aug 2022 16:54:15: 30000000 INFO @ Tue, 02 Aug 2022 16:54:15: 26000000 INFO @ Tue, 02 Aug 2022 16:54:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:54:22: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:54:22: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:54:22: #1 total tags in treatment: 14942205 INFO @ Tue, 02 Aug 2022 16:54:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:54:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:54:23: #1 tags after filtering in treatment: 13796344 INFO @ Tue, 02 Aug 2022 16:54:23: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 16:54:23: #1 finished! INFO @ Tue, 02 Aug 2022 16:54:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:54:23: 27000000 INFO @ Tue, 02 Aug 2022 16:54:24: #2 number of paired peaks: 1983 INFO @ Tue, 02 Aug 2022 16:54:24: start model_add_line... INFO @ Tue, 02 Aug 2022 16:54:24: start X-correlation... INFO @ Tue, 02 Aug 2022 16:54:24: end of X-cor INFO @ Tue, 02 Aug 2022 16:54:24: #2 finished! INFO @ Tue, 02 Aug 2022 16:54:24: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 16:54:24: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 02 Aug 2022 16:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.10_model.r INFO @ Tue, 02 Aug 2022 16:54:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:54:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:54:30: 28000000 INFO @ Tue, 02 Aug 2022 16:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.05_summits.bed INFO @ Tue, 02 Aug 2022 16:54:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5501 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:54:36: 29000000 INFO @ Tue, 02 Aug 2022 16:54:42: 30000000 INFO @ Tue, 02 Aug 2022 16:54:49: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:54:49: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:54:49: #1 total tags in treatment: 14942205 INFO @ Tue, 02 Aug 2022 16:54:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:54:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:54:49: #1 tags after filtering in treatment: 13796344 INFO @ Tue, 02 Aug 2022 16:54:49: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 16:54:49: #1 finished! INFO @ Tue, 02 Aug 2022 16:54:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:54:50: #2 number of paired peaks: 1983 INFO @ Tue, 02 Aug 2022 16:54:50: start model_add_line... INFO @ Tue, 02 Aug 2022 16:54:50: start X-correlation... INFO @ Tue, 02 Aug 2022 16:54:50: end of X-cor INFO @ Tue, 02 Aug 2022 16:54:50: #2 finished! INFO @ Tue, 02 Aug 2022 16:54:50: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 16:54:50: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 02 Aug 2022 16:54:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.20_model.r INFO @ Tue, 02 Aug 2022 16:54:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:54:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:54:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.10_summits.bed INFO @ Tue, 02 Aug 2022 16:55:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3403 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:55:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518343/SRX9518343.20_summits.bed INFO @ Tue, 02 Aug 2022 16:55:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1491 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。