Job ID = 6626517 SRX = SRX5736491 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10516545 spots for SRR8956902/SRR8956902.sra Written 10516545 spots for SRR8956902/SRR8956902.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626700 ("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: 00:23:14 10516545 reads; of these: 10516545 (100.00%) were paired; of these: 1180824 (11.23%) aligned concordantly 0 times 6798276 (64.64%) aligned concordantly exactly 1 time 2537445 (24.13%) aligned concordantly >1 times ---- 1180824 pairs aligned concordantly 0 times; of these: 319437 (27.05%) aligned discordantly 1 time ---- 861387 pairs aligned 0 times concordantly or discordantly; of these: 1722774 mates make up the pairs; of these: 1134001 (65.82%) aligned 0 times 286959 (16.66%) aligned exactly 1 time 301814 (17.52%) aligned >1 times 94.61% overall alignment rate Time searching: 00:23:14 Overall time: 00:23:14 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] 694372 / 9635637 = 0.0721 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.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, 14 Jul 2020 07:46:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:46:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:46:58: 1000000 INFO @ Tue, 14 Jul 2020 07:47:04: 2000000 INFO @ Tue, 14 Jul 2020 07:47:10: 3000000 INFO @ Tue, 14 Jul 2020 07:47:16: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.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, 14 Jul 2020 07:47:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:47:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:47:22: 5000000 INFO @ Tue, 14 Jul 2020 07:47:28: 1000000 INFO @ Tue, 14 Jul 2020 07:47:28: 6000000 INFO @ Tue, 14 Jul 2020 07:47:34: 2000000 INFO @ Tue, 14 Jul 2020 07:47:34: 7000000 INFO @ Tue, 14 Jul 2020 07:47:41: 3000000 INFO @ Tue, 14 Jul 2020 07:47:41: 8000000 INFO @ Tue, 14 Jul 2020 07:47:47: 4000000 INFO @ Tue, 14 Jul 2020 07:47:48: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:47:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.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, 14 Jul 2020 07:47:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:47:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:47:54: 5000000 INFO @ Tue, 14 Jul 2020 07:47:54: 10000000 INFO @ Tue, 14 Jul 2020 07:47:58: 1000000 INFO @ Tue, 14 Jul 2020 07:48:00: 6000000 INFO @ Tue, 14 Jul 2020 07:48:00: 11000000 INFO @ Tue, 14 Jul 2020 07:48:05: 2000000 INFO @ Tue, 14 Jul 2020 07:48:06: 7000000 INFO @ Tue, 14 Jul 2020 07:48:07: 12000000 INFO @ Tue, 14 Jul 2020 07:48:11: 3000000 INFO @ Tue, 14 Jul 2020 07:48:13: 8000000 INFO @ Tue, 14 Jul 2020 07:48:13: 13000000 INFO @ Tue, 14 Jul 2020 07:48:18: 4000000 INFO @ Tue, 14 Jul 2020 07:48:19: 9000000 INFO @ Tue, 14 Jul 2020 07:48:20: 14000000 INFO @ Tue, 14 Jul 2020 07:48:25: 5000000 INFO @ Tue, 14 Jul 2020 07:48:25: 10000000 INFO @ Tue, 14 Jul 2020 07:48:26: 15000000 INFO @ Tue, 14 Jul 2020 07:48:31: 6000000 INFO @ Tue, 14 Jul 2020 07:48:32: 11000000 INFO @ Tue, 14 Jul 2020 07:48:32: 16000000 INFO @ Tue, 14 Jul 2020 07:48:38: 7000000 INFO @ Tue, 14 Jul 2020 07:48:38: 12000000 INFO @ Tue, 14 Jul 2020 07:48:39: 17000000 INFO @ Tue, 14 Jul 2020 07:48:44: 8000000 INFO @ Tue, 14 Jul 2020 07:48:44: 13000000 INFO @ Tue, 14 Jul 2020 07:48:45: 18000000 INFO @ Tue, 14 Jul 2020 07:48:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:48:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:48:50: #1 total tags in treatment: 8670012 INFO @ Tue, 14 Jul 2020 07:48:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:48:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:48:50: #1 tags after filtering in treatment: 8020069 INFO @ Tue, 14 Jul 2020 07:48:50: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:48:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:48:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:48:50: #2 number of paired peaks: 200 WARNING @ Tue, 14 Jul 2020 07:48:50: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 14 Jul 2020 07:48:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:48:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:48:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:48:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:48:50: #2 predicted fragment length is 153 bps INFO @ Tue, 14 Jul 2020 07:48:50: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 14 Jul 2020 07:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.05_model.r INFO @ Tue, 14 Jul 2020 07:48:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:48:51: 9000000 INFO @ Tue, 14 Jul 2020 07:48:53: 14000000 INFO @ Tue, 14 Jul 2020 07:48:57: 10000000 INFO @ Tue, 14 Jul 2020 07:49:02: 15000000 INFO @ Tue, 14 Jul 2020 07:49:03: 11000000 INFO @ Tue, 14 Jul 2020 07:49:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:10: 12000000 INFO @ Tue, 14 Jul 2020 07:49:12: 16000000 INFO @ Tue, 14 Jul 2020 07:49:16: 13000000 INFO @ Tue, 14 Jul 2020 07:49:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:49:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:49:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.05_summits.bed INFO @ Tue, 14 Jul 2020 07:49:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2885 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:49:22: 17000000 INFO @ Tue, 14 Jul 2020 07:49:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:49:29: 15000000 INFO @ Tue, 14 Jul 2020 07:49:30: 18000000 INFO @ Tue, 14 Jul 2020 07:49:34: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:49:34: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:49:34: #1 total tags in treatment: 8670012 INFO @ Tue, 14 Jul 2020 07:49:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:49:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:49:34: #1 tags after filtering in treatment: 8020069 INFO @ Tue, 14 Jul 2020 07:49:34: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:49:34: #1 finished! INFO @ Tue, 14 Jul 2020 07:49:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:49:34: #2 number of paired peaks: 200 WARNING @ Tue, 14 Jul 2020 07:49:34: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 14 Jul 2020 07:49:34: start model_add_line... INFO @ Tue, 14 Jul 2020 07:49:35: start X-correlation... INFO @ Tue, 14 Jul 2020 07:49:35: end of X-cor INFO @ Tue, 14 Jul 2020 07:49:35: #2 finished! INFO @ Tue, 14 Jul 2020 07:49:35: #2 predicted fragment length is 153 bps INFO @ Tue, 14 Jul 2020 07:49:35: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 14 Jul 2020 07:49:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.10_model.r INFO @ Tue, 14 Jul 2020 07:49:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:49:36: 16000000 INFO @ Tue, 14 Jul 2020 07:49:42: 17000000 INFO @ Tue, 14 Jul 2020 07:49:48: 18000000 INFO @ Tue, 14 Jul 2020 07:49:51: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:49:51: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:49:51: #1 total tags in treatment: 8670012 INFO @ Tue, 14 Jul 2020 07:49:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:49:51: #1 tags after filtering in treatment: 8020069 INFO @ Tue, 14 Jul 2020 07:49:51: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:49:51: #1 finished! INFO @ Tue, 14 Jul 2020 07:49:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:49:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:52: #2 number of paired peaks: 200 WARNING @ Tue, 14 Jul 2020 07:49:52: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 14 Jul 2020 07:49:52: start model_add_line... INFO @ Tue, 14 Jul 2020 07:49:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:49:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:49:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:49:52: #2 predicted fragment length is 153 bps INFO @ Tue, 14 Jul 2020 07:49:52: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 14 Jul 2020 07:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.20_model.r INFO @ Tue, 14 Jul 2020 07:49:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.10_summits.bed INFO @ Tue, 14 Jul 2020 07:50:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:50:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:50:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:50:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:50:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736491/SRX5736491.20_summits.bed INFO @ Tue, 14 Jul 2020 07:50:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (456 records, 4 fields): 11 millis CompletedMACS2peakCalling