Job ID = 16440143 SRX = SRX12178823 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T08:20:48 prefetch.2.10.7: 1) Downloading 'SRR15888091'... 2022-08-02T08:20:48 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T08:21:57 prefetch.2.10.7: HTTPS download succeed 2022-08-02T08:21:57 prefetch.2.10.7: 1) 'SRR15888091' was downloaded successfully 2022-08-02T08:21:57 prefetch.2.10.7: 'SRR15888091' has 0 unresolved dependencies Read 25753079 spots for SRR15888091/SRR15888091.sra Written 25753079 spots for SRR15888091/SRR15888091.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440851 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:30:53 25753079 reads; of these: 25753079 (100.00%) were paired; of these: 9365623 (36.37%) aligned concordantly 0 times 14089623 (54.71%) aligned concordantly exactly 1 time 2297833 (8.92%) aligned concordantly >1 times ---- 9365623 pairs aligned concordantly 0 times; of these: 3368668 (35.97%) aligned discordantly 1 time ---- 5996955 pairs aligned 0 times concordantly or discordantly; of these: 11993910 mates make up the pairs; of these: 8573250 (71.48%) aligned 0 times 2558650 (21.33%) aligned exactly 1 time 862010 (7.19%) aligned >1 times 83.35% overall alignment rate Time searching: 00:30:54 Overall time: 00:30:54 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] 3935233 / 19687043 = 0.1999 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 18:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.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 18:08:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:08:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:08:46: 1000000 INFO @ Tue, 02 Aug 2022 18:08:52: 2000000 INFO @ Tue, 02 Aug 2022 18:08:58: 3000000 INFO @ Tue, 02 Aug 2022 18:09:04: 4000000 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 18:09:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.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 18:09:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:09:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:09:10: 5000000 INFO @ Tue, 02 Aug 2022 18:09:16: 1000000 INFO @ Tue, 02 Aug 2022 18:09:17: 6000000 INFO @ Tue, 02 Aug 2022 18:09:22: 2000000 INFO @ Tue, 02 Aug 2022 18:09:24: 7000000 INFO @ Tue, 02 Aug 2022 18:09:28: 3000000 INFO @ Tue, 02 Aug 2022 18:09:30: 8000000 INFO @ Tue, 02 Aug 2022 18:09:35: 4000000 INFO @ Tue, 02 Aug 2022 18:09:37: 9000000 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 18:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.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 18:09:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:09:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:09:41: 5000000 INFO @ Tue, 02 Aug 2022 18:09:43: 10000000 INFO @ Tue, 02 Aug 2022 18:09:44: 1000000 INFO @ Tue, 02 Aug 2022 18:09:48: 6000000 INFO @ Tue, 02 Aug 2022 18:09:49: 2000000 INFO @ Tue, 02 Aug 2022 18:09:50: 11000000 INFO @ Tue, 02 Aug 2022 18:09:54: 7000000 INFO @ Tue, 02 Aug 2022 18:09:55: 3000000 INFO @ Tue, 02 Aug 2022 18:09:56: 12000000 INFO @ Tue, 02 Aug 2022 18:10:00: 4000000 INFO @ Tue, 02 Aug 2022 18:10:01: 8000000 INFO @ Tue, 02 Aug 2022 18:10:03: 13000000 INFO @ Tue, 02 Aug 2022 18:10:05: 5000000 INFO @ Tue, 02 Aug 2022 18:10:08: 9000000 INFO @ Tue, 02 Aug 2022 18:10:10: 14000000 INFO @ Tue, 02 Aug 2022 18:10:11: 6000000 INFO @ Tue, 02 Aug 2022 18:10:14: 10000000 INFO @ Tue, 02 Aug 2022 18:10:16: 7000000 INFO @ Tue, 02 Aug 2022 18:10:17: 15000000 INFO @ Tue, 02 Aug 2022 18:10:21: 11000000 INFO @ Tue, 02 Aug 2022 18:10:21: 8000000 INFO @ Tue, 02 Aug 2022 18:10:23: 16000000 INFO @ Tue, 02 Aug 2022 18:10:27: 9000000 INFO @ Tue, 02 Aug 2022 18:10:27: 12000000 INFO @ Tue, 02 Aug 2022 18:10:30: 17000000 INFO @ Tue, 02 Aug 2022 18:10:32: 10000000 INFO @ Tue, 02 Aug 2022 18:10:34: 13000000 INFO @ Tue, 02 Aug 2022 18:10:36: 18000000 INFO @ Tue, 02 Aug 2022 18:10:37: 11000000 INFO @ Tue, 02 Aug 2022 18:10:40: 14000000 INFO @ Tue, 02 Aug 2022 18:10:42: 12000000 INFO @ Tue, 02 Aug 2022 18:10:43: 19000000 INFO @ Tue, 02 Aug 2022 18:10:47: 13000000 INFO @ Tue, 02 Aug 2022 18:10:47: 15000000 INFO @ Tue, 02 Aug 2022 18:10:49: 20000000 INFO @ Tue, 02 Aug 2022 18:10:52: 14000000 INFO @ Tue, 02 Aug 2022 18:10:54: 16000000 INFO @ Tue, 02 Aug 2022 18:10:56: 21000000 INFO @ Tue, 02 Aug 2022 18:10:57: 15000000 INFO @ Tue, 02 Aug 2022 18:11:00: 17000000 INFO @ Tue, 02 Aug 2022 18:11:02: 16000000 INFO @ Tue, 02 Aug 2022 18:11:03: 22000000 INFO @ Tue, 02 Aug 2022 18:11:06: 18000000 INFO @ Tue, 02 Aug 2022 18:11:07: 17000000 INFO @ Tue, 02 Aug 2022 18:11:09: 23000000 INFO @ Tue, 02 Aug 2022 18:11:12: 18000000 INFO @ Tue, 02 Aug 2022 18:11:13: 19000000 INFO @ Tue, 02 Aug 2022 18:11:16: 24000000 INFO @ Tue, 02 Aug 2022 18:11:17: 19000000 INFO @ Tue, 02 Aug 2022 18:11:19: 20000000 INFO @ Tue, 02 Aug 2022 18:11:22: 20000000 INFO @ Tue, 02 Aug 2022 18:11:22: 25000000 INFO @ Tue, 02 Aug 2022 18:11:25: 21000000 INFO @ Tue, 02 Aug 2022 18:11:27: 21000000 INFO @ Tue, 02 Aug 2022 18:11:29: 26000000 INFO @ Tue, 02 Aug 2022 18:11:32: 22000000 INFO @ Tue, 02 Aug 2022 18:11:32: 22000000 INFO @ Tue, 02 Aug 2022 18:11:35: 27000000 INFO @ Tue, 02 Aug 2022 18:11:37: 23000000 INFO @ Tue, 02 Aug 2022 18:11:38: 23000000 INFO @ Tue, 02 Aug 2022 18:11:42: 24000000 INFO @ Tue, 02 Aug 2022 18:11:42: 28000000 INFO @ Tue, 02 Aug 2022 18:11:45: 24000000 INFO @ Tue, 02 Aug 2022 18:11:47: 25000000 INFO @ Tue, 02 Aug 2022 18:11:49: 29000000 INFO @ Tue, 02 Aug 2022 18:11:51: 25000000 INFO @ Tue, 02 Aug 2022 18:11:52: 26000000 INFO @ Tue, 02 Aug 2022 18:11:55: 30000000 INFO @ Tue, 02 Aug 2022 18:11:57: 27000000 INFO @ Tue, 02 Aug 2022 18:11:57: 26000000 INFO @ Tue, 02 Aug 2022 18:12:02: 31000000 INFO @ Tue, 02 Aug 2022 18:12:02: 28000000 INFO @ Tue, 02 Aug 2022 18:12:03: 27000000 INFO @ Tue, 02 Aug 2022 18:12:07: 29000000 INFO @ Tue, 02 Aug 2022 18:12:08: 32000000 INFO @ Tue, 02 Aug 2022 18:12:10: 28000000 INFO @ Tue, 02 Aug 2022 18:12:12: 30000000 INFO @ Tue, 02 Aug 2022 18:12:15: 33000000 INFO @ Tue, 02 Aug 2022 18:12:16: 29000000 INFO @ Tue, 02 Aug 2022 18:12:17: 31000000 INFO @ Tue, 02 Aug 2022 18:12:22: 34000000 INFO @ Tue, 02 Aug 2022 18:12:22: 32000000 INFO @ Tue, 02 Aug 2022 18:12:22: 30000000 INFO @ Tue, 02 Aug 2022 18:12:27: 33000000 INFO @ Tue, 02 Aug 2022 18:12:29: 35000000 INFO @ Tue, 02 Aug 2022 18:12:29: 31000000 INFO @ Tue, 02 Aug 2022 18:12:29: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 18:12:29: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 18:12:29: #1 total tags in treatment: 12980245 INFO @ Tue, 02 Aug 2022 18:12:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:12:29: #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 18:12:29: #1 tags after filtering in treatment: 9596184 INFO @ Tue, 02 Aug 2022 18:12:29: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 18:12:29: #1 finished! INFO @ Tue, 02 Aug 2022 18:12:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:12:30: #2 number of paired peaks: 2104 INFO @ Tue, 02 Aug 2022 18:12:30: start model_add_line... INFO @ Tue, 02 Aug 2022 18:12:30: start X-correlation... INFO @ Tue, 02 Aug 2022 18:12:31: end of X-cor INFO @ Tue, 02 Aug 2022 18:12:31: #2 finished! INFO @ Tue, 02 Aug 2022 18:12:31: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 18:12:31: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 02 Aug 2022 18:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.05_model.r WARNING @ Tue, 02 Aug 2022 18:12:31: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:12:31: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 02 Aug 2022 18:12:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:12:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:12:33: 34000000 INFO @ Tue, 02 Aug 2022 18:12:35: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:12:38: 35000000 INFO @ Tue, 02 Aug 2022 18:12:38: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 18:12:38: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 18:12:38: #1 total tags in treatment: 12980245 INFO @ Tue, 02 Aug 2022 18:12:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:12:38: #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 18:12:38: #1 tags after filtering in treatment: 9596184 INFO @ Tue, 02 Aug 2022 18:12:38: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 18:12:38: #1 finished! INFO @ Tue, 02 Aug 2022 18:12:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:12:39: #2 number of paired peaks: 2104 INFO @ Tue, 02 Aug 2022 18:12:39: start model_add_line... INFO @ Tue, 02 Aug 2022 18:12:39: start X-correlation... INFO @ Tue, 02 Aug 2022 18:12:39: end of X-cor INFO @ Tue, 02 Aug 2022 18:12:39: #2 finished! INFO @ Tue, 02 Aug 2022 18:12:39: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 18:12:39: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 02 Aug 2022 18:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.20_model.r WARNING @ Tue, 02 Aug 2022 18:12:39: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:12:39: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 02 Aug 2022 18:12:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:12:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:12:41: 33000000 INFO @ Tue, 02 Aug 2022 18:12:47: 34000000 INFO @ Tue, 02 Aug 2022 18:12:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:12:53: 35000000 INFO @ Tue, 02 Aug 2022 18:12:53: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 18:12:53: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 18:12:53: #1 total tags in treatment: 12980245 INFO @ Tue, 02 Aug 2022 18:12:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:12:53: #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 18:12:53: #1 tags after filtering in treatment: 9596184 INFO @ Tue, 02 Aug 2022 18:12:53: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 18:12:53: #1 finished! INFO @ Tue, 02 Aug 2022 18:12:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:12:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:12:54: #2 number of paired peaks: 2104 INFO @ Tue, 02 Aug 2022 18:12:54: start model_add_line... INFO @ Tue, 02 Aug 2022 18:12:54: start X-correlation... INFO @ Tue, 02 Aug 2022 18:12:54: end of X-cor INFO @ Tue, 02 Aug 2022 18:12:54: #2 finished! INFO @ Tue, 02 Aug 2022 18:12:54: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 18:12:54: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 02 Aug 2022 18:12:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.10_model.r WARNING @ Tue, 02 Aug 2022 18:12:54: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:12:54: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 02 Aug 2022 18:12:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:12:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:12:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:12:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:13:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.05_summits.bed INFO @ Tue, 02 Aug 2022 18:13:02: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (15155 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.20_summits.bed INFO @ Tue, 02 Aug 2022 18:13:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (884 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:13:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178823/SRX12178823.10_summits.bed INFO @ Tue, 02 Aug 2022 18:13:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7129 records, 4 fields): 39 millis CompletedMACS2peakCalling BigWig に変換しました。