Job ID = 16436208 SRX = SRX12178859 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:05:58 prefetch.2.10.7: 1) Downloading 'SRR15888055'... 2022-08-02T02:05:58 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:07:09 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:07:09 prefetch.2.10.7: 1) 'SRR15888055' was downloaded successfully 2022-08-02T02:07:09 prefetch.2.10.7: 'SRR15888055' has 0 unresolved dependencies Read 25023095 spots for SRR15888055/SRR15888055.sra Written 25023095 spots for SRR15888055/SRR15888055.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436565 ("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: 00:22:44 25023095 reads; of these: 25023095 (100.00%) were paired; of these: 7248178 (28.97%) aligned concordantly 0 times 12636383 (50.50%) aligned concordantly exactly 1 time 5138534 (20.54%) aligned concordantly >1 times ---- 7248178 pairs aligned concordantly 0 times; of these: 1733330 (23.91%) aligned discordantly 1 time ---- 5514848 pairs aligned 0 times concordantly or discordantly; of these: 11029696 mates make up the pairs; of these: 6679050 (60.56%) aligned 0 times 3045356 (27.61%) aligned exactly 1 time 1305290 (11.83%) aligned >1 times 86.65% overall alignment rate Time searching: 00:22:44 Overall time: 00:22:44 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] 4005970 / 19441569 = 0.2061 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 11:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.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 11:42:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:42:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:42:29: 1000000 INFO @ Tue, 02 Aug 2022 11:42:35: 2000000 INFO @ Tue, 02 Aug 2022 11:42:40: 3000000 INFO @ Tue, 02 Aug 2022 11:42:45: 4000000 INFO @ Tue, 02 Aug 2022 11:42:50: 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 11:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.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 11:42:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:42:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:42:55: 6000000 INFO @ Tue, 02 Aug 2022 11:42:58: 1000000 INFO @ Tue, 02 Aug 2022 11:43:01: 7000000 INFO @ Tue, 02 Aug 2022 11:43:03: 2000000 INFO @ Tue, 02 Aug 2022 11:43:06: 8000000 INFO @ Tue, 02 Aug 2022 11:43:08: 3000000 INFO @ Tue, 02 Aug 2022 11:43:11: 9000000 INFO @ Tue, 02 Aug 2022 11:43:13: 4000000 INFO @ Tue, 02 Aug 2022 11:43:17: 10000000 INFO @ Tue, 02 Aug 2022 11:43:18: 5000000 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 11:43:22: 11000000 INFO @ Tue, 02 Aug 2022 11:43:23: 6000000 INFO @ Tue, 02 Aug 2022 11:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.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 11:43:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:43:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:43:28: 7000000 INFO @ Tue, 02 Aug 2022 11:43:28: 12000000 INFO @ Tue, 02 Aug 2022 11:43:28: 1000000 INFO @ Tue, 02 Aug 2022 11:43:33: 8000000 INFO @ Tue, 02 Aug 2022 11:43:34: 2000000 INFO @ Tue, 02 Aug 2022 11:43:34: 13000000 INFO @ Tue, 02 Aug 2022 11:43:38: 9000000 INFO @ Tue, 02 Aug 2022 11:43:39: 3000000 INFO @ Tue, 02 Aug 2022 11:43:39: 14000000 INFO @ Tue, 02 Aug 2022 11:43:43: 10000000 INFO @ Tue, 02 Aug 2022 11:43:44: 4000000 INFO @ Tue, 02 Aug 2022 11:43:45: 15000000 INFO @ Tue, 02 Aug 2022 11:43:49: 11000000 INFO @ Tue, 02 Aug 2022 11:43:49: 5000000 INFO @ Tue, 02 Aug 2022 11:43:51: 16000000 INFO @ Tue, 02 Aug 2022 11:43:54: 12000000 INFO @ Tue, 02 Aug 2022 11:43:55: 6000000 INFO @ Tue, 02 Aug 2022 11:43:57: 17000000 INFO @ Tue, 02 Aug 2022 11:43:59: 13000000 INFO @ Tue, 02 Aug 2022 11:44:01: 7000000 INFO @ Tue, 02 Aug 2022 11:44:03: 18000000 INFO @ Tue, 02 Aug 2022 11:44:04: 14000000 INFO @ Tue, 02 Aug 2022 11:44:06: 8000000 INFO @ Tue, 02 Aug 2022 11:44:09: 19000000 INFO @ Tue, 02 Aug 2022 11:44:09: 15000000 INFO @ Tue, 02 Aug 2022 11:44:11: 9000000 INFO @ Tue, 02 Aug 2022 11:44:15: 20000000 INFO @ Tue, 02 Aug 2022 11:44:15: 16000000 INFO @ Tue, 02 Aug 2022 11:44:16: 10000000 INFO @ Tue, 02 Aug 2022 11:44:19: 21000000 INFO @ Tue, 02 Aug 2022 11:44:20: 17000000 INFO @ Tue, 02 Aug 2022 11:44:22: 11000000 INFO @ Tue, 02 Aug 2022 11:44:24: 22000000 INFO @ Tue, 02 Aug 2022 11:44:25: 18000000 INFO @ Tue, 02 Aug 2022 11:44:27: 12000000 INFO @ Tue, 02 Aug 2022 11:44:29: 23000000 INFO @ Tue, 02 Aug 2022 11:44:30: 19000000 INFO @ Tue, 02 Aug 2022 11:44:32: 13000000 INFO @ Tue, 02 Aug 2022 11:44:35: 20000000 INFO @ Tue, 02 Aug 2022 11:44:35: 24000000 INFO @ Tue, 02 Aug 2022 11:44:37: 14000000 INFO @ Tue, 02 Aug 2022 11:44:40: 21000000 INFO @ Tue, 02 Aug 2022 11:44:41: 25000000 INFO @ Tue, 02 Aug 2022 11:44:42: 15000000 INFO @ Tue, 02 Aug 2022 11:44:45: 22000000 INFO @ Tue, 02 Aug 2022 11:44:47: 26000000 INFO @ Tue, 02 Aug 2022 11:44:47: 16000000 INFO @ Tue, 02 Aug 2022 11:44:50: 23000000 INFO @ Tue, 02 Aug 2022 11:44:52: 27000000 INFO @ Tue, 02 Aug 2022 11:44:52: 17000000 INFO @ Tue, 02 Aug 2022 11:44:55: 24000000 INFO @ Tue, 02 Aug 2022 11:44:57: 18000000 INFO @ Tue, 02 Aug 2022 11:44:58: 28000000 INFO @ Tue, 02 Aug 2022 11:45:00: 25000000 INFO @ Tue, 02 Aug 2022 11:45:02: 19000000 INFO @ Tue, 02 Aug 2022 11:45:03: 29000000 INFO @ Tue, 02 Aug 2022 11:45:05: 26000000 INFO @ Tue, 02 Aug 2022 11:45:07: 20000000 INFO @ Tue, 02 Aug 2022 11:45:10: 27000000 INFO @ Tue, 02 Aug 2022 11:45:10: 30000000 INFO @ Tue, 02 Aug 2022 11:45:12: 21000000 INFO @ Tue, 02 Aug 2022 11:45:14: 28000000 INFO @ Tue, 02 Aug 2022 11:45:16: 31000000 INFO @ Tue, 02 Aug 2022 11:45:17: 22000000 INFO @ Tue, 02 Aug 2022 11:45:19: 29000000 INFO @ Tue, 02 Aug 2022 11:45:21: 32000000 INFO @ Tue, 02 Aug 2022 11:45:22: 23000000 INFO @ Tue, 02 Aug 2022 11:45:24: 30000000 INFO @ Tue, 02 Aug 2022 11:45:26: 33000000 INFO @ Tue, 02 Aug 2022 11:45:27: 24000000 INFO @ Tue, 02 Aug 2022 11:45:29: 31000000 INFO @ Tue, 02 Aug 2022 11:45:31: 34000000 INFO @ Tue, 02 Aug 2022 11:45:32: 25000000 INFO @ Tue, 02 Aug 2022 11:45:34: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:45:36: 35000000 INFO @ Tue, 02 Aug 2022 11:45:37: 26000000 INFO @ Tue, 02 Aug 2022 11:45:37: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:45:37: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:45:37: #1 total tags in treatment: 13894191 INFO @ Tue, 02 Aug 2022 11:45:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:45:37: #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 11:45:38: #1 tags after filtering in treatment: 10382886 INFO @ Tue, 02 Aug 2022 11:45:38: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 11:45:38: #1 finished! INFO @ Tue, 02 Aug 2022 11:45:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:45:38: #2 number of paired peaks: 750 WARNING @ Tue, 02 Aug 2022 11:45:38: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Tue, 02 Aug 2022 11:45:38: start model_add_line... INFO @ Tue, 02 Aug 2022 11:45:39: start X-correlation... INFO @ Tue, 02 Aug 2022 11:45:39: end of X-cor INFO @ Tue, 02 Aug 2022 11:45:39: #2 finished! INFO @ Tue, 02 Aug 2022 11:45:39: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 11:45:39: #2 alternative fragment length(s) may be 108,115,118 bps INFO @ Tue, 02 Aug 2022 11:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.05_model.r INFO @ Tue, 02 Aug 2022 11:45:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:45:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:45:39: 33000000 INFO @ Tue, 02 Aug 2022 11:45:42: 27000000 INFO @ Tue, 02 Aug 2022 11:45:44: 34000000 INFO @ Tue, 02 Aug 2022 11:45:46: 28000000 INFO @ Tue, 02 Aug 2022 11:45:49: 35000000 INFO @ Tue, 02 Aug 2022 11:45:51: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:45:51: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:45:51: #1 total tags in treatment: 13894191 INFO @ Tue, 02 Aug 2022 11:45:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:45:51: #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 11:45:51: #1 tags after filtering in treatment: 10382886 INFO @ Tue, 02 Aug 2022 11:45:51: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 11:45:51: #1 finished! INFO @ Tue, 02 Aug 2022 11:45:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:45:51: 29000000 INFO @ Tue, 02 Aug 2022 11:45:52: #2 number of paired peaks: 750 WARNING @ Tue, 02 Aug 2022 11:45:52: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Tue, 02 Aug 2022 11:45:52: start model_add_line... INFO @ Tue, 02 Aug 2022 11:45:52: start X-correlation... INFO @ Tue, 02 Aug 2022 11:45:52: end of X-cor INFO @ Tue, 02 Aug 2022 11:45:52: #2 finished! INFO @ Tue, 02 Aug 2022 11:45:52: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 11:45:52: #2 alternative fragment length(s) may be 108,115,118 bps INFO @ Tue, 02 Aug 2022 11:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.10_model.r INFO @ Tue, 02 Aug 2022 11:45:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:45:56: 30000000 INFO @ Tue, 02 Aug 2022 11:45:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:46:00: 31000000 INFO @ Tue, 02 Aug 2022 11:46:05: 32000000 INFO @ Tue, 02 Aug 2022 11:46:09: 33000000 INFO @ Tue, 02 Aug 2022 11:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.05_summits.bed INFO @ Tue, 02 Aug 2022 11:46:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9220 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:46:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:46:14: 34000000 INFO @ Tue, 02 Aug 2022 11:46:18: 35000000 INFO @ Tue, 02 Aug 2022 11:46:20: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:46:20: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:46:20: #1 total tags in treatment: 13894191 INFO @ Tue, 02 Aug 2022 11:46:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:46:20: #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 11:46:20: #1 tags after filtering in treatment: 10382886 INFO @ Tue, 02 Aug 2022 11:46:20: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 11:46:20: #1 finished! INFO @ Tue, 02 Aug 2022 11:46:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:46:21: #2 number of paired peaks: 750 WARNING @ Tue, 02 Aug 2022 11:46:21: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Tue, 02 Aug 2022 11:46:21: start model_add_line... INFO @ Tue, 02 Aug 2022 11:46:21: start X-correlation... INFO @ Tue, 02 Aug 2022 11:46:21: end of X-cor INFO @ Tue, 02 Aug 2022 11:46:21: #2 finished! INFO @ Tue, 02 Aug 2022 11:46:21: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 11:46:21: #2 alternative fragment length(s) may be 108,115,118 bps INFO @ Tue, 02 Aug 2022 11:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.20_model.r INFO @ Tue, 02 Aug 2022 11:46:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.10_summits.bed INFO @ Tue, 02 Aug 2022 11:46:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4539 records, 4 fields): 71 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:46:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178859/SRX12178859.20_summits.bed INFO @ Tue, 02 Aug 2022 11:46:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (921 records, 4 fields): 105 millis CompletedMACS2peakCalling