Job ID = 14171036 SRX = SRX11704595 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T00:13:05 prefetch.2.10.7: 1) Downloading 'SRR15402379'... 2021-12-11T00:13:05 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T00:13:51 prefetch.2.10.7: HTTPS download succeed 2021-12-11T00:13:51 prefetch.2.10.7: 1) 'SRR15402379' was downloaded successfully 2021-12-11T00:13:51 prefetch.2.10.7: 'SRR15402379' has 0 unresolved dependencies Read 20606379 spots for SRR15402379/SRR15402379.sra Written 20606379 spots for SRR15402379/SRR15402379.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171513 ("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: 00:12:20 20606379 reads; of these: 20606379 (100.00%) were paired; of these: 9643149 (46.80%) aligned concordantly 0 times 9991172 (48.49%) aligned concordantly exactly 1 time 972058 (4.72%) aligned concordantly >1 times ---- 9643149 pairs aligned concordantly 0 times; of these: 1360652 (14.11%) aligned discordantly 1 time ---- 8282497 pairs aligned 0 times concordantly or discordantly; of these: 16564994 mates make up the pairs; of these: 15325302 (92.52%) aligned 0 times 835734 (5.05%) aligned exactly 1 time 403958 (2.44%) aligned >1 times 62.81% overall alignment rate Time searching: 00:12:20 Overall time: 00:12:20 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 12 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] 2093503 / 12250126 = 0.1709 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.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 @ Sat, 11 Dec 2021 09:36:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:36:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:36:56: 1000000 INFO @ Sat, 11 Dec 2021 09:37:01: 2000000 INFO @ Sat, 11 Dec 2021 09:37:05: 3000000 INFO @ Sat, 11 Dec 2021 09:37:09: 4000000 INFO @ Sat, 11 Dec 2021 09:37:14: 5000000 INFO @ Sat, 11 Dec 2021 09:37:18: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.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 @ Sat, 11 Dec 2021 09:37:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:37:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:37:22: 7000000 INFO @ Sat, 11 Dec 2021 09:37:26: 1000000 INFO @ Sat, 11 Dec 2021 09:37:27: 8000000 INFO @ Sat, 11 Dec 2021 09:37:31: 2000000 INFO @ Sat, 11 Dec 2021 09:37:31: 9000000 INFO @ Sat, 11 Dec 2021 09:37:35: 3000000 INFO @ Sat, 11 Dec 2021 09:37:36: 10000000 INFO @ Sat, 11 Dec 2021 09:37:39: 4000000 INFO @ Sat, 11 Dec 2021 09:37:40: 11000000 INFO @ Sat, 11 Dec 2021 09:37:43: 5000000 INFO @ Sat, 11 Dec 2021 09:37:44: 12000000 INFO @ Sat, 11 Dec 2021 09:37:48: 6000000 BedGraph に変換中... INFO @ Sat, 11 Dec 2021 09:37:49: 13000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.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 @ Sat, 11 Dec 2021 09:37:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:37:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:37:53: 7000000 INFO @ Sat, 11 Dec 2021 09:37:54: 14000000 INFO @ Sat, 11 Dec 2021 09:37:57: 8000000 INFO @ Sat, 11 Dec 2021 09:37:57: 1000000 INFO @ Sat, 11 Dec 2021 09:37:58: 15000000 INFO @ Sat, 11 Dec 2021 09:38:02: 9000000 INFO @ Sat, 11 Dec 2021 09:38:02: 2000000 INFO @ Sat, 11 Dec 2021 09:38:03: 16000000 INFO @ Sat, 11 Dec 2021 09:38:06: 10000000 INFO @ Sat, 11 Dec 2021 09:38:07: 17000000 INFO @ Sat, 11 Dec 2021 09:38:08: 3000000 INFO @ Sat, 11 Dec 2021 09:38:11: 11000000 INFO @ Sat, 11 Dec 2021 09:38:12: 18000000 INFO @ Sat, 11 Dec 2021 09:38:13: 4000000 INFO @ Sat, 11 Dec 2021 09:38:16: 12000000 INFO @ Sat, 11 Dec 2021 09:38:16: 19000000 INFO @ Sat, 11 Dec 2021 09:38:18: 5000000 INFO @ Sat, 11 Dec 2021 09:38:21: 13000000 INFO @ Sat, 11 Dec 2021 09:38:21: 20000000 INFO @ Sat, 11 Dec 2021 09:38:23: 6000000 INFO @ Sat, 11 Dec 2021 09:38:25: 14000000 INFO @ Sat, 11 Dec 2021 09:38:25: 21000000 INFO @ Sat, 11 Dec 2021 09:38:28: 7000000 INFO @ Sat, 11 Dec 2021 09:38:29: #1 tag size is determined as 38 bps INFO @ Sat, 11 Dec 2021 09:38:29: #1 tag size = 38 INFO @ Sat, 11 Dec 2021 09:38:29: #1 total tags in treatment: 9107452 INFO @ Sat, 11 Dec 2021 09:38:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:38:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:38:29: #1 tags after filtering in treatment: 5914354 INFO @ Sat, 11 Dec 2021 09:38:29: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 09:38:29: #1 finished! INFO @ Sat, 11 Dec 2021 09:38:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:38:30: #2 number of paired peaks: 5578 INFO @ Sat, 11 Dec 2021 09:38:30: start model_add_line... INFO @ Sat, 11 Dec 2021 09:38:30: start X-correlation... INFO @ Sat, 11 Dec 2021 09:38:30: end of X-cor INFO @ Sat, 11 Dec 2021 09:38:30: #2 finished! INFO @ Sat, 11 Dec 2021 09:38:30: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 09:38:30: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 09:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.05_model.r INFO @ Sat, 11 Dec 2021 09:38:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:38:30: 15000000 INFO @ Sat, 11 Dec 2021 09:38:33: 8000000 INFO @ Sat, 11 Dec 2021 09:38:35: 16000000 INFO @ Sat, 11 Dec 2021 09:38:38: 9000000 INFO @ Sat, 11 Dec 2021 09:38:40: 17000000 INFO @ Sat, 11 Dec 2021 09:38:43: 10000000 INFO @ Sat, 11 Dec 2021 09:38:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:38:44: 18000000 INFO @ Sat, 11 Dec 2021 09:38:47: 11000000 INFO @ Sat, 11 Dec 2021 09:38:49: 19000000 INFO @ Sat, 11 Dec 2021 09:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.05_summits.bed INFO @ Sat, 11 Dec 2021 09:38:51: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (19491 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:38:52: 12000000 INFO @ Sat, 11 Dec 2021 09:38:54: 20000000 INFO @ Sat, 11 Dec 2021 09:38:57: 13000000 INFO @ Sat, 11 Dec 2021 09:38:59: 21000000 INFO @ Sat, 11 Dec 2021 09:39:02: 14000000 INFO @ Sat, 11 Dec 2021 09:39:02: #1 tag size is determined as 38 bps INFO @ Sat, 11 Dec 2021 09:39:02: #1 tag size = 38 INFO @ Sat, 11 Dec 2021 09:39:02: #1 total tags in treatment: 9107452 INFO @ Sat, 11 Dec 2021 09:39:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:39:03: #1 tags after filtering in treatment: 5914354 INFO @ Sat, 11 Dec 2021 09:39:03: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 09:39:03: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:03: #2 number of paired peaks: 5578 INFO @ Sat, 11 Dec 2021 09:39:03: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:03: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:04: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:04: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:04: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 09:39:04: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 09:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.10_model.r INFO @ Sat, 11 Dec 2021 09:39:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:39:06: 15000000 INFO @ Sat, 11 Dec 2021 09:39:10: 16000000 INFO @ Sat, 11 Dec 2021 09:39:15: 17000000 INFO @ Sat, 11 Dec 2021 09:39:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:39:19: 18000000 INFO @ Sat, 11 Dec 2021 09:39:23: 19000000 INFO @ Sat, 11 Dec 2021 09:39:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.10_summits.bed INFO @ Sat, 11 Dec 2021 09:39:25: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11897 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:39:28: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:39:32: 21000000 INFO @ Sat, 11 Dec 2021 09:39:35: #1 tag size is determined as 38 bps INFO @ Sat, 11 Dec 2021 09:39:35: #1 tag size = 38 INFO @ Sat, 11 Dec 2021 09:39:35: #1 total tags in treatment: 9107452 INFO @ Sat, 11 Dec 2021 09:39:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:39:35: #1 tags after filtering in treatment: 5914354 INFO @ Sat, 11 Dec 2021 09:39:35: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 09:39:35: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:36: #2 number of paired peaks: 5578 INFO @ Sat, 11 Dec 2021 09:39:36: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:36: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:36: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:36: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:36: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 09:39:36: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 09:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.20_model.r INFO @ Sat, 11 Dec 2021 09:39:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:39:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:39:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:39:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:39:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704595/SRX11704595.20_summits.bed INFO @ Sat, 11 Dec 2021 09:39:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5464 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。