Job ID = 14170750 SRX = SRX11704568 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T23:21:50 prefetch.2.10.7: 1) Downloading 'SRR15402352'... 2021-12-10T23:21:50 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T23:25:52 prefetch.2.10.7: HTTPS download succeed 2021-12-10T23:25:52 prefetch.2.10.7: 1) 'SRR15402352' was downloaded successfully 2021-12-10T23:25:52 prefetch.2.10.7: 'SRR15402352' has 0 unresolved dependencies Read 111965019 spots for SRR15402352/SRR15402352.sra Written 111965019 spots for SRR15402352/SRR15402352.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171532 ("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: 00:57:48 111965019 reads; of these: 111965019 (100.00%) were paired; of these: 94753620 (84.63%) aligned concordantly 0 times 13762083 (12.29%) aligned concordantly exactly 1 time 3449316 (3.08%) aligned concordantly >1 times ---- 94753620 pairs aligned concordantly 0 times; of these: 3554771 (3.75%) aligned discordantly 1 time ---- 91198849 pairs aligned 0 times concordantly or discordantly; of these: 182397698 mates make up the pairs; of these: 179596538 (98.46%) aligned 0 times 1103570 (0.61%) aligned exactly 1 time 1697590 (0.93%) aligned >1 times 19.80% overall alignment rate Time searching: 00:57:48 Overall time: 00:57:48 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 20 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] 5415506 / 20331762 = 0.2664 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 09:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.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 09:47:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:47:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:47:48: 1000000 INFO @ Sat, 11 Dec 2021 09:47:56: 2000000 INFO @ Sat, 11 Dec 2021 09:48:03: 3000000 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 09:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.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 09:48:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:48:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:48:11: 4000000 INFO @ Sat, 11 Dec 2021 09:48:19: 5000000 INFO @ Sat, 11 Dec 2021 09:48:20: 1000000 INFO @ Sat, 11 Dec 2021 09:48:27: 6000000 INFO @ Sat, 11 Dec 2021 09:48:31: 2000000 INFO @ Sat, 11 Dec 2021 09:48:36: 7000000 BedGraph に変換中... 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 09:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.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 09:48:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:48:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:48:43: 3000000 INFO @ Sat, 11 Dec 2021 09:48:44: 8000000 INFO @ Sat, 11 Dec 2021 09:48:49: 1000000 INFO @ Sat, 11 Dec 2021 09:48:52: 9000000 INFO @ Sat, 11 Dec 2021 09:48:54: 4000000 INFO @ Sat, 11 Dec 2021 09:48:58: 2000000 INFO @ Sat, 11 Dec 2021 09:49:00: 10000000 INFO @ Sat, 11 Dec 2021 09:49:05: 5000000 INFO @ Sat, 11 Dec 2021 09:49:08: 3000000 INFO @ Sat, 11 Dec 2021 09:49:08: 11000000 INFO @ Sat, 11 Dec 2021 09:49:16: 6000000 INFO @ Sat, 11 Dec 2021 09:49:16: 12000000 INFO @ Sat, 11 Dec 2021 09:49:17: 4000000 INFO @ Sat, 11 Dec 2021 09:49:24: 13000000 INFO @ Sat, 11 Dec 2021 09:49:27: 7000000 INFO @ Sat, 11 Dec 2021 09:49:27: 5000000 INFO @ Sat, 11 Dec 2021 09:49:33: 14000000 INFO @ Sat, 11 Dec 2021 09:49:37: 6000000 INFO @ Sat, 11 Dec 2021 09:49:37: 8000000 INFO @ Sat, 11 Dec 2021 09:49:41: 15000000 INFO @ Sat, 11 Dec 2021 09:49:46: 7000000 INFO @ Sat, 11 Dec 2021 09:49:48: 9000000 INFO @ Sat, 11 Dec 2021 09:49:48: 16000000 INFO @ Sat, 11 Dec 2021 09:49:55: 8000000 INFO @ Sat, 11 Dec 2021 09:49:56: 17000000 INFO @ Sat, 11 Dec 2021 09:49:59: 10000000 INFO @ Sat, 11 Dec 2021 09:50:04: 18000000 INFO @ Sat, 11 Dec 2021 09:50:05: 9000000 INFO @ Sat, 11 Dec 2021 09:50:11: 11000000 INFO @ Sat, 11 Dec 2021 09:50:13: 19000000 INFO @ Sat, 11 Dec 2021 09:50:14: 10000000 INFO @ Sat, 11 Dec 2021 09:50:21: 20000000 INFO @ Sat, 11 Dec 2021 09:50:22: 12000000 INFO @ Sat, 11 Dec 2021 09:50:24: 11000000 INFO @ Sat, 11 Dec 2021 09:50:29: 21000000 INFO @ Sat, 11 Dec 2021 09:50:33: 12000000 INFO @ Sat, 11 Dec 2021 09:50:34: 13000000 INFO @ Sat, 11 Dec 2021 09:50:38: 22000000 INFO @ Sat, 11 Dec 2021 09:50:43: 13000000 INFO @ Sat, 11 Dec 2021 09:50:44: 14000000 INFO @ Sat, 11 Dec 2021 09:50:46: 23000000 INFO @ Sat, 11 Dec 2021 09:50:52: 14000000 INFO @ Sat, 11 Dec 2021 09:50:54: 24000000 INFO @ Sat, 11 Dec 2021 09:50:55: 15000000 INFO @ Sat, 11 Dec 2021 09:51:02: 15000000 INFO @ Sat, 11 Dec 2021 09:51:02: 25000000 INFO @ Sat, 11 Dec 2021 09:51:06: 16000000 INFO @ Sat, 11 Dec 2021 09:51:10: 26000000 INFO @ Sat, 11 Dec 2021 09:51:11: 16000000 INFO @ Sat, 11 Dec 2021 09:51:17: 17000000 INFO @ Sat, 11 Dec 2021 09:51:18: 27000000 INFO @ Sat, 11 Dec 2021 09:51:21: 17000000 INFO @ Sat, 11 Dec 2021 09:51:26: 28000000 INFO @ Sat, 11 Dec 2021 09:51:28: 18000000 INFO @ Sat, 11 Dec 2021 09:51:30: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:51:34: 29000000 INFO @ Sat, 11 Dec 2021 09:51:40: 19000000 INFO @ Sat, 11 Dec 2021 09:51:40: 19000000 INFO @ Sat, 11 Dec 2021 09:51:42: 30000000 INFO @ Sat, 11 Dec 2021 09:51:50: 20000000 INFO @ Sat, 11 Dec 2021 09:51:51: 20000000 INFO @ Sat, 11 Dec 2021 09:51:51: 31000000 INFO @ Sat, 11 Dec 2021 09:51:59: 32000000 INFO @ Sat, 11 Dec 2021 09:51:59: 21000000 INFO @ Sat, 11 Dec 2021 09:52:02: 21000000 INFO @ Sat, 11 Dec 2021 09:52:07: 33000000 INFO @ Sat, 11 Dec 2021 09:52:09: 22000000 INFO @ Sat, 11 Dec 2021 09:52:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:52:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:52:12: #1 total tags in treatment: 12985069 INFO @ Sat, 11 Dec 2021 09:52:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:52:12: #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 09:52:12: #1 tags after filtering in treatment: 9631527 INFO @ Sat, 11 Dec 2021 09:52:12: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 09:52:12: #1 finished! INFO @ Sat, 11 Dec 2021 09:52:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:52:12: 22000000 INFO @ Sat, 11 Dec 2021 09:52:13: #2 number of paired peaks: 1865 INFO @ Sat, 11 Dec 2021 09:52:13: start model_add_line... INFO @ Sat, 11 Dec 2021 09:52:13: start X-correlation... INFO @ Sat, 11 Dec 2021 09:52:13: end of X-cor INFO @ Sat, 11 Dec 2021 09:52:13: #2 finished! INFO @ Sat, 11 Dec 2021 09:52:13: #2 predicted fragment length is 69 bps INFO @ Sat, 11 Dec 2021 09:52:13: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 11 Dec 2021 09:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.05_model.r WARNING @ Sat, 11 Dec 2021 09:52:13: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:52:13: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 11 Dec 2021 09:52:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:52:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:52:19: 23000000 INFO @ Sat, 11 Dec 2021 09:52:23: 23000000 INFO @ Sat, 11 Dec 2021 09:52:28: 24000000 INFO @ Sat, 11 Dec 2021 09:52:34: 24000000 INFO @ Sat, 11 Dec 2021 09:52:37: 25000000 INFO @ Sat, 11 Dec 2021 09:52:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:52:45: 25000000 INFO @ Sat, 11 Dec 2021 09:52:47: 26000000 INFO @ Sat, 11 Dec 2021 09:52:56: 26000000 INFO @ Sat, 11 Dec 2021 09:52:56: 27000000 INFO @ Sat, 11 Dec 2021 09:52:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:52:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:52:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.05_summits.bed INFO @ Sat, 11 Dec 2021 09:52:57: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (14256 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:53:05: 28000000 INFO @ Sat, 11 Dec 2021 09:53:07: 27000000 INFO @ Sat, 11 Dec 2021 09:53:15: 29000000 INFO @ Sat, 11 Dec 2021 09:53:17: 28000000 INFO @ Sat, 11 Dec 2021 09:53:24: 30000000 INFO @ Sat, 11 Dec 2021 09:53:28: 29000000 INFO @ Sat, 11 Dec 2021 09:53:33: 31000000 INFO @ Sat, 11 Dec 2021 09:53:38: 30000000 INFO @ Sat, 11 Dec 2021 09:53:42: 32000000 INFO @ Sat, 11 Dec 2021 09:53:49: 31000000 INFO @ Sat, 11 Dec 2021 09:53:52: 33000000 INFO @ Sat, 11 Dec 2021 09:53:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:53:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:53:56: #1 total tags in treatment: 12985069 INFO @ Sat, 11 Dec 2021 09:53:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:53:56: #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 09:53:57: #1 tags after filtering in treatment: 9631527 INFO @ Sat, 11 Dec 2021 09:53:57: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 09:53:57: #1 finished! INFO @ Sat, 11 Dec 2021 09:53:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:53:58: #2 number of paired peaks: 1865 INFO @ Sat, 11 Dec 2021 09:53:58: start model_add_line... INFO @ Sat, 11 Dec 2021 09:53:58: start X-correlation... INFO @ Sat, 11 Dec 2021 09:53:58: end of X-cor INFO @ Sat, 11 Dec 2021 09:53:58: #2 finished! INFO @ Sat, 11 Dec 2021 09:53:58: #2 predicted fragment length is 69 bps INFO @ Sat, 11 Dec 2021 09:53:58: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 11 Dec 2021 09:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.20_model.r WARNING @ Sat, 11 Dec 2021 09:53:58: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:53:58: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 11 Dec 2021 09:53:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:53:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:53:59: 32000000 INFO @ Sat, 11 Dec 2021 09:54:09: 33000000 INFO @ Sat, 11 Dec 2021 09:54:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:54:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:54:14: #1 total tags in treatment: 12985069 INFO @ Sat, 11 Dec 2021 09:54:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:54:14: #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 09:54:14: #1 tags after filtering in treatment: 9631527 INFO @ Sat, 11 Dec 2021 09:54:14: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 09:54:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:54:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:54:15: #2 number of paired peaks: 1865 INFO @ Sat, 11 Dec 2021 09:54:15: start model_add_line... INFO @ Sat, 11 Dec 2021 09:54:15: start X-correlation... INFO @ Sat, 11 Dec 2021 09:54:15: end of X-cor INFO @ Sat, 11 Dec 2021 09:54:15: #2 finished! INFO @ Sat, 11 Dec 2021 09:54:15: #2 predicted fragment length is 69 bps INFO @ Sat, 11 Dec 2021 09:54:15: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 11 Dec 2021 09:54:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.10_model.r WARNING @ Sat, 11 Dec 2021 09:54:15: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:54:15: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 11 Dec 2021 09:54:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:54:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:54:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.20_summits.bed INFO @ Sat, 11 Dec 2021 09:54:41: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3286 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:54:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704568/SRX11704568.10_summits.bed INFO @ Sat, 11 Dec 2021 09:54:57: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8654 records, 4 fields): 18 millis CompletedMACS2peakCalling