Job ID = 6626496 SRX = SRX5736475 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8311679 spots for SRR8956886/SRR8956886.sra Written 8311679 spots for SRR8956886/SRR8956886.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626672 ("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: 00:21:23 8311679 reads; of these: 8311679 (100.00%) were paired; of these: 2701619 (32.50%) aligned concordantly 0 times 3983059 (47.92%) aligned concordantly exactly 1 time 1627001 (19.57%) aligned concordantly >1 times ---- 2701619 pairs aligned concordantly 0 times; of these: 1251903 (46.34%) aligned discordantly 1 time ---- 1449716 pairs aligned 0 times concordantly or discordantly; of these: 2899432 mates make up the pairs; of these: 1490222 (51.40%) aligned 0 times 530492 (18.30%) aligned exactly 1 time 878718 (30.31%) aligned >1 times 91.04% overall alignment rate Time searching: 00:21:23 Overall time: 00:21:23 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 8 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] 656044 / 6835403 = 0.0960 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 07:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.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 07:35:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:31: 1000000 INFO @ Tue, 14 Jul 2020 07:35:40: 2000000 INFO @ Tue, 14 Jul 2020 07:35:48: 3000000 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 07:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.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 07:35:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:57: 4000000 INFO @ Tue, 14 Jul 2020 07:35:59: 1000000 INFO @ Tue, 14 Jul 2020 07:36:06: 5000000 INFO @ Tue, 14 Jul 2020 07:36:06: 2000000 INFO @ Tue, 14 Jul 2020 07:36:14: 3000000 INFO @ Tue, 14 Jul 2020 07:36:16: 6000000 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 07:36:21: 4000000 INFO @ Tue, 14 Jul 2020 07:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.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 07:36:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:25: 7000000 INFO @ Tue, 14 Jul 2020 07:36:29: 5000000 INFO @ Tue, 14 Jul 2020 07:36:30: 1000000 INFO @ Tue, 14 Jul 2020 07:36:35: 8000000 INFO @ Tue, 14 Jul 2020 07:36:37: 6000000 INFO @ Tue, 14 Jul 2020 07:36:38: 2000000 INFO @ Tue, 14 Jul 2020 07:36:43: 9000000 INFO @ Tue, 14 Jul 2020 07:36:45: 7000000 INFO @ Tue, 14 Jul 2020 07:36:47: 3000000 INFO @ Tue, 14 Jul 2020 07:36:51: 10000000 INFO @ Tue, 14 Jul 2020 07:36:53: 8000000 INFO @ Tue, 14 Jul 2020 07:36:55: 4000000 INFO @ Tue, 14 Jul 2020 07:37:00: 11000000 INFO @ Tue, 14 Jul 2020 07:37:01: 9000000 INFO @ Tue, 14 Jul 2020 07:37:04: 5000000 INFO @ Tue, 14 Jul 2020 07:37:08: 12000000 INFO @ Tue, 14 Jul 2020 07:37:10: 10000000 INFO @ Tue, 14 Jul 2020 07:37:12: 6000000 INFO @ Tue, 14 Jul 2020 07:37:16: 13000000 INFO @ Tue, 14 Jul 2020 07:37:18: 11000000 INFO @ Tue, 14 Jul 2020 07:37:21: 7000000 INFO @ Tue, 14 Jul 2020 07:37:23: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:37:23: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:37:23: #1 total tags in treatment: 5082609 INFO @ Tue, 14 Jul 2020 07:37:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:23: #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 07:37:23: #1 tags after filtering in treatment: 4707576 INFO @ Tue, 14 Jul 2020 07:37:23: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:37:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:23: #2 number of paired peaks: 359 WARNING @ Tue, 14 Jul 2020 07:37:23: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 14 Jul 2020 07:37:23: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:23: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:23: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:23: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:23: #2 predicted fragment length is 156 bps INFO @ Tue, 14 Jul 2020 07:37:23: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 14 Jul 2020 07:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.05_model.r INFO @ Tue, 14 Jul 2020 07:37:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:26: 12000000 INFO @ Tue, 14 Jul 2020 07:37:30: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:37:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:34: 13000000 INFO @ Tue, 14 Jul 2020 07:37:38: 9000000 INFO @ Tue, 14 Jul 2020 07:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.05_summits.bed INFO @ Tue, 14 Jul 2020 07:37:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1437 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:37:41: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:37:41: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:37:41: #1 total tags in treatment: 5082609 INFO @ Tue, 14 Jul 2020 07:37:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:41: #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 07:37:41: #1 tags after filtering in treatment: 4707576 INFO @ Tue, 14 Jul 2020 07:37:41: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:37:41: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:41: #2 number of paired peaks: 359 WARNING @ Tue, 14 Jul 2020 07:37:41: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 14 Jul 2020 07:37:41: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:41: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:41: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:41: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:41: #2 predicted fragment length is 156 bps INFO @ Tue, 14 Jul 2020 07:37:41: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 14 Jul 2020 07:37:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.10_model.r INFO @ Tue, 14 Jul 2020 07:37:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:47: 10000000 INFO @ Tue, 14 Jul 2020 07:37:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:55: 11000000 INFO @ Tue, 14 Jul 2020 07:37:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.10_summits.bed INFO @ Tue, 14 Jul 2020 07:37:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (737 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:38:03: 12000000 INFO @ Tue, 14 Jul 2020 07:38:11: 13000000 INFO @ Tue, 14 Jul 2020 07:38:18: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:38:18: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:38:18: #1 total tags in treatment: 5082609 INFO @ Tue, 14 Jul 2020 07:38:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:38:18: #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 07:38:18: #1 tags after filtering in treatment: 4707576 INFO @ Tue, 14 Jul 2020 07:38:18: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:38:18: #1 finished! INFO @ Tue, 14 Jul 2020 07:38:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:38:18: #2 number of paired peaks: 359 WARNING @ Tue, 14 Jul 2020 07:38:18: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 14 Jul 2020 07:38:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:38:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:38:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:38:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:38:18: #2 predicted fragment length is 156 bps INFO @ Tue, 14 Jul 2020 07:38:18: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 14 Jul 2020 07:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.20_model.r INFO @ Tue, 14 Jul 2020 07:38:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:38:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736475/SRX5736475.20_summits.bed INFO @ Tue, 14 Jul 2020 07:38:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 38 millis CompletedMACS2peakCalling