Job ID = 16437418 SRX = ERX9180698 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:23:30 prefetch.2.10.7: 1) Downloading 'ERR9627606'... 2022-08-02T03:23:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:24:29 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:24:29 prefetch.2.10.7: 1) 'ERR9627606' was downloaded successfully 2022-08-02T03:24:29 prefetch.2.10.7: 'ERR9627606' has 0 unresolved dependencies Read 28108827 spots for ERR9627606/ERR9627606.sra Written 28108827 spots for ERR9627606/ERR9627606.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437601 ("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: 00:22:16 28108827 reads; of these: 28108827 (100.00%) were paired; of these: 18328570 (65.21%) aligned concordantly 0 times 7603408 (27.05%) aligned concordantly exactly 1 time 2176849 (7.74%) aligned concordantly >1 times ---- 18328570 pairs aligned concordantly 0 times; of these: 2313058 (12.62%) aligned discordantly 1 time ---- 16015512 pairs aligned 0 times concordantly or discordantly; of these: 32031024 mates make up the pairs; of these: 27953507 (87.27%) aligned 0 times 2204720 (6.88%) aligned exactly 1 time 1872797 (5.85%) aligned >1 times 50.28% overall alignment rate Time searching: 00:22:16 Overall time: 00:22:16 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] 777377 / 11777588 = 0.0660 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 12:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.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 12:55:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:55:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:55:53: 1000000 INFO @ Tue, 02 Aug 2022 12:55:57: 2000000 INFO @ Tue, 02 Aug 2022 12:56:02: 3000000 INFO @ Tue, 02 Aug 2022 12:56:06: 4000000 INFO @ Tue, 02 Aug 2022 12:56:11: 5000000 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 12:56:15: 6000000 INFO @ Tue, 02 Aug 2022 12:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.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 12:56:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:56:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:56:20: 7000000 INFO @ Tue, 02 Aug 2022 12:56:20: 1000000 INFO @ Tue, 02 Aug 2022 12:56:24: 2000000 INFO @ Tue, 02 Aug 2022 12:56:24: 8000000 INFO @ Tue, 02 Aug 2022 12:56:29: 3000000 INFO @ Tue, 02 Aug 2022 12:56:29: 9000000 INFO @ Tue, 02 Aug 2022 12:56:33: 4000000 INFO @ Tue, 02 Aug 2022 12:56:34: 10000000 INFO @ Tue, 02 Aug 2022 12:56:37: 5000000 INFO @ Tue, 02 Aug 2022 12:56:38: 11000000 INFO @ Tue, 02 Aug 2022 12:56:41: 6000000 INFO @ Tue, 02 Aug 2022 12:56:43: 12000000 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 12:56:46: 7000000 INFO @ Tue, 02 Aug 2022 12:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.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 12:56:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:56:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:56:47: 13000000 INFO @ Tue, 02 Aug 2022 12:56:50: 8000000 INFO @ Tue, 02 Aug 2022 12:56:50: 1000000 INFO @ Tue, 02 Aug 2022 12:56:52: 14000000 INFO @ Tue, 02 Aug 2022 12:56:54: 9000000 INFO @ Tue, 02 Aug 2022 12:56:54: 2000000 INFO @ Tue, 02 Aug 2022 12:56:57: 15000000 INFO @ Tue, 02 Aug 2022 12:56:58: 10000000 INFO @ Tue, 02 Aug 2022 12:56:59: 3000000 INFO @ Tue, 02 Aug 2022 12:57:01: 16000000 INFO @ Tue, 02 Aug 2022 12:57:03: 11000000 INFO @ Tue, 02 Aug 2022 12:57:03: 4000000 INFO @ Tue, 02 Aug 2022 12:57:06: 17000000 INFO @ Tue, 02 Aug 2022 12:57:07: 12000000 INFO @ Tue, 02 Aug 2022 12:57:07: 5000000 INFO @ Tue, 02 Aug 2022 12:57:10: 18000000 INFO @ Tue, 02 Aug 2022 12:57:11: 13000000 INFO @ Tue, 02 Aug 2022 12:57:11: 6000000 INFO @ Tue, 02 Aug 2022 12:57:15: 19000000 INFO @ Tue, 02 Aug 2022 12:57:15: 14000000 INFO @ Tue, 02 Aug 2022 12:57:16: 7000000 INFO @ Tue, 02 Aug 2022 12:57:19: 20000000 INFO @ Tue, 02 Aug 2022 12:57:20: 15000000 INFO @ Tue, 02 Aug 2022 12:57:20: 8000000 INFO @ Tue, 02 Aug 2022 12:57:24: 16000000 INFO @ Tue, 02 Aug 2022 12:57:24: 9000000 INFO @ Tue, 02 Aug 2022 12:57:24: 21000000 INFO @ Tue, 02 Aug 2022 12:57:28: 17000000 INFO @ Tue, 02 Aug 2022 12:57:28: 10000000 INFO @ Tue, 02 Aug 2022 12:57:29: 22000000 INFO @ Tue, 02 Aug 2022 12:57:32: 18000000 INFO @ Tue, 02 Aug 2022 12:57:33: 11000000 INFO @ Tue, 02 Aug 2022 12:57:34: 23000000 INFO @ Tue, 02 Aug 2022 12:57:37: 19000000 INFO @ Tue, 02 Aug 2022 12:57:37: 12000000 INFO @ Tue, 02 Aug 2022 12:57:39: 24000000 INFO @ Tue, 02 Aug 2022 12:57:41: 13000000 INFO @ Tue, 02 Aug 2022 12:57:41: 20000000 INFO @ Tue, 02 Aug 2022 12:57:44: 25000000 INFO @ Tue, 02 Aug 2022 12:57:45: 14000000 INFO @ Tue, 02 Aug 2022 12:57:46: 21000000 INFO @ Tue, 02 Aug 2022 12:57:49: 26000000 INFO @ Tue, 02 Aug 2022 12:57:50: 15000000 INFO @ Tue, 02 Aug 2022 12:57:50: 22000000 INFO @ Tue, 02 Aug 2022 12:57:52: #1 tag size is determined as 41 bps INFO @ Tue, 02 Aug 2022 12:57:52: #1 tag size = 41 INFO @ Tue, 02 Aug 2022 12:57:52: #1 total tags in treatment: 9094578 INFO @ Tue, 02 Aug 2022 12:57:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:57:52: #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 12:57:52: #1 tags after filtering in treatment: 8188655 INFO @ Tue, 02 Aug 2022 12:57:52: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 02 Aug 2022 12:57:52: #1 finished! INFO @ Tue, 02 Aug 2022 12:57:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:57:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:57:53: #2 number of paired peaks: 7500 INFO @ Tue, 02 Aug 2022 12:57:53: start model_add_line... INFO @ Tue, 02 Aug 2022 12:57:53: start X-correlation... INFO @ Tue, 02 Aug 2022 12:57:53: end of X-cor INFO @ Tue, 02 Aug 2022 12:57:53: #2 finished! INFO @ Tue, 02 Aug 2022 12:57:53: #2 predicted fragment length is 153 bps INFO @ Tue, 02 Aug 2022 12:57:53: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 02 Aug 2022 12:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.05_model.r INFO @ Tue, 02 Aug 2022 12:57:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:57:54: 16000000 INFO @ Tue, 02 Aug 2022 12:57:54: 23000000 INFO @ Tue, 02 Aug 2022 12:57:58: 17000000 INFO @ Tue, 02 Aug 2022 12:57:58: 24000000 INFO @ Tue, 02 Aug 2022 12:58:02: 18000000 INFO @ Tue, 02 Aug 2022 12:58:02: 25000000 INFO @ Tue, 02 Aug 2022 12:58:06: 19000000 INFO @ Tue, 02 Aug 2022 12:58:07: 26000000 INFO @ Tue, 02 Aug 2022 12:58:10: #1 tag size is determined as 41 bps INFO @ Tue, 02 Aug 2022 12:58:10: #1 tag size = 41 INFO @ Tue, 02 Aug 2022 12:58:10: #1 total tags in treatment: 9094578 INFO @ Tue, 02 Aug 2022 12:58:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:58:10: #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 12:58:10: #1 tags after filtering in treatment: 8188655 INFO @ Tue, 02 Aug 2022 12:58:10: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 02 Aug 2022 12:58:10: #1 finished! INFO @ Tue, 02 Aug 2022 12:58:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:58:10: 20000000 INFO @ Tue, 02 Aug 2022 12:58:11: #2 number of paired peaks: 7500 INFO @ Tue, 02 Aug 2022 12:58:11: start model_add_line... INFO @ Tue, 02 Aug 2022 12:58:11: start X-correlation... INFO @ Tue, 02 Aug 2022 12:58:11: end of X-cor INFO @ Tue, 02 Aug 2022 12:58:11: #2 finished! INFO @ Tue, 02 Aug 2022 12:58:11: #2 predicted fragment length is 153 bps INFO @ Tue, 02 Aug 2022 12:58:11: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 02 Aug 2022 12:58:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.10_model.r INFO @ Tue, 02 Aug 2022 12:58:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:58:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:58:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:58:15: 21000000 INFO @ Tue, 02 Aug 2022 12:58:19: 22000000 INFO @ Tue, 02 Aug 2022 12:58:23: 23000000 INFO @ Tue, 02 Aug 2022 12:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.05_summits.bed INFO @ Tue, 02 Aug 2022 12:58:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8994 records, 4 fields): 74 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:58:27: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:58:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:58:31: 25000000 INFO @ Tue, 02 Aug 2022 12:58:35: 26000000 INFO @ Tue, 02 Aug 2022 12:58:37: #1 tag size is determined as 41 bps INFO @ Tue, 02 Aug 2022 12:58:37: #1 tag size = 41 INFO @ Tue, 02 Aug 2022 12:58:37: #1 total tags in treatment: 9094578 INFO @ Tue, 02 Aug 2022 12:58:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:58:37: #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 12:58:38: #1 tags after filtering in treatment: 8188655 INFO @ Tue, 02 Aug 2022 12:58:38: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 02 Aug 2022 12:58:38: #1 finished! INFO @ Tue, 02 Aug 2022 12:58:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:58:39: #2 number of paired peaks: 7500 INFO @ Tue, 02 Aug 2022 12:58:39: start model_add_line... INFO @ Tue, 02 Aug 2022 12:58:39: start X-correlation... INFO @ Tue, 02 Aug 2022 12:58:39: end of X-cor INFO @ Tue, 02 Aug 2022 12:58:39: #2 finished! INFO @ Tue, 02 Aug 2022 12:58:39: #2 predicted fragment length is 153 bps INFO @ Tue, 02 Aug 2022 12:58:39: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 02 Aug 2022 12:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.20_model.r INFO @ Tue, 02 Aug 2022 12:58:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.10_summits.bed INFO @ Tue, 02 Aug 2022 12:58:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6988 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:58:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:59:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180698/ERX9180698.20_summits.bed INFO @ Tue, 02 Aug 2022 12:59:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4123 records, 4 fields): 91 millis CompletedMACS2peakCalling