Job ID = 6626473 SRX = SRX5736458 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16121391 spots for SRR8956869/SRR8956869.sra Written 16121391 spots for SRR8956869/SRR8956869.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626664 ("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: 00:20:43 16121391 reads; of these: 16121391 (100.00%) were paired; of these: 8715096 (54.06%) aligned concordantly 0 times 5591477 (34.68%) aligned concordantly exactly 1 time 1814818 (11.26%) aligned concordantly >1 times ---- 8715096 pairs aligned concordantly 0 times; of these: 126637 (1.45%) aligned discordantly 1 time ---- 8588459 pairs aligned 0 times concordantly or discordantly; of these: 17176918 mates make up the pairs; of these: 16708871 (97.28%) aligned 0 times 159166 (0.93%) aligned exactly 1 time 308881 (1.80%) aligned >1 times 48.18% overall alignment rate Time searching: 00:20:43 Overall time: 00:20:43 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] 1126587 / 7522883 = 0.1498 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 07:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.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 07:30:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:30:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:57: 1000000 INFO @ Tue, 14 Jul 2020 07:31:02: 2000000 INFO @ Tue, 14 Jul 2020 07:31:08: 3000000 INFO @ Tue, 14 Jul 2020 07:31:14: 4000000 INFO @ Tue, 14 Jul 2020 07:31:19: 5000000 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 07:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.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 07:31:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:31:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:31:25: 6000000 INFO @ Tue, 14 Jul 2020 07:31:27: 1000000 INFO @ Tue, 14 Jul 2020 07:31:31: 7000000 INFO @ Tue, 14 Jul 2020 07:31:33: 2000000 INFO @ Tue, 14 Jul 2020 07:31:37: 8000000 INFO @ Tue, 14 Jul 2020 07:31:39: 3000000 INFO @ Tue, 14 Jul 2020 07:31:42: 9000000 INFO @ Tue, 14 Jul 2020 07:31:45: 4000000 INFO @ Tue, 14 Jul 2020 07:31:49: 10000000 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 07:31:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.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 07:31:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:31:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:31:52: 5000000 INFO @ Tue, 14 Jul 2020 07:31:56: 11000000 INFO @ Tue, 14 Jul 2020 07:31:58: 1000000 INFO @ Tue, 14 Jul 2020 07:31:59: 6000000 INFO @ Tue, 14 Jul 2020 07:32:02: 12000000 INFO @ Tue, 14 Jul 2020 07:32:05: 2000000 INFO @ Tue, 14 Jul 2020 07:32:05: 7000000 INFO @ Tue, 14 Jul 2020 07:32:09: 13000000 INFO @ Tue, 14 Jul 2020 07:32:10: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:32:10: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:32:10: #1 total tags in treatment: 6287953 INFO @ Tue, 14 Jul 2020 07:32:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:32:10: #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 07:32:11: #1 tags after filtering in treatment: 5757513 INFO @ Tue, 14 Jul 2020 07:32:11: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:32:11: #1 finished! INFO @ Tue, 14 Jul 2020 07:32:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:32:11: #2 number of paired peaks: 724 WARNING @ Tue, 14 Jul 2020 07:32:11: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Tue, 14 Jul 2020 07:32:11: start model_add_line... INFO @ Tue, 14 Jul 2020 07:32:11: start X-correlation... INFO @ Tue, 14 Jul 2020 07:32:11: end of X-cor INFO @ Tue, 14 Jul 2020 07:32:11: #2 finished! INFO @ Tue, 14 Jul 2020 07:32:11: #2 predicted fragment length is 236 bps INFO @ Tue, 14 Jul 2020 07:32:11: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 14 Jul 2020 07:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.05_model.r INFO @ Tue, 14 Jul 2020 07:32:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:32:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:32:12: 3000000 INFO @ Tue, 14 Jul 2020 07:32:12: 8000000 INFO @ Tue, 14 Jul 2020 07:32:18: 9000000 INFO @ Tue, 14 Jul 2020 07:32:19: 4000000 INFO @ Tue, 14 Jul 2020 07:32:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:32:25: 10000000 INFO @ Tue, 14 Jul 2020 07:32:26: 5000000 INFO @ Tue, 14 Jul 2020 07:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:32:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:32:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.05_summits.bed INFO @ Tue, 14 Jul 2020 07:32:30: Done! INFO @ Tue, 14 Jul 2020 07:32:31: 11000000 INFO @ Tue, 14 Jul 2020 07:32:33: 6000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8217 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:32:38: 12000000 INFO @ Tue, 14 Jul 2020 07:32:40: 7000000 INFO @ Tue, 14 Jul 2020 07:32:44: 13000000 INFO @ Tue, 14 Jul 2020 07:32:46: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:32:46: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:32:46: #1 total tags in treatment: 6287953 INFO @ Tue, 14 Jul 2020 07:32:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:32:46: #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 07:32:46: #1 tags after filtering in treatment: 5757513 INFO @ Tue, 14 Jul 2020 07:32:46: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:32:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:32:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:32:46: #2 number of paired peaks: 724 WARNING @ Tue, 14 Jul 2020 07:32:46: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Tue, 14 Jul 2020 07:32:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:32:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:32:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:32:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:32:46: #2 predicted fragment length is 236 bps INFO @ Tue, 14 Jul 2020 07:32:46: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 14 Jul 2020 07:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.10_model.r INFO @ Tue, 14 Jul 2020 07:32:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:32:46: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:32:53: 9000000 INFO @ Tue, 14 Jul 2020 07:32:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:33:00: 10000000 INFO @ Tue, 14 Jul 2020 07:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.10_summits.bed INFO @ Tue, 14 Jul 2020 07:33:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2505 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:33:06: 11000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:33:13: 12000000 INFO @ Tue, 14 Jul 2020 07:33:20: 13000000 INFO @ Tue, 14 Jul 2020 07:33:21: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:33:21: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:33:21: #1 total tags in treatment: 6287953 INFO @ Tue, 14 Jul 2020 07:33:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:33:21: #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 07:33:21: #1 tags after filtering in treatment: 5757513 INFO @ Tue, 14 Jul 2020 07:33:21: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:33:21: #1 finished! INFO @ Tue, 14 Jul 2020 07:33:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:33:22: #2 number of paired peaks: 724 WARNING @ Tue, 14 Jul 2020 07:33:22: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Tue, 14 Jul 2020 07:33:22: start model_add_line... INFO @ Tue, 14 Jul 2020 07:33:22: start X-correlation... INFO @ Tue, 14 Jul 2020 07:33:22: end of X-cor INFO @ Tue, 14 Jul 2020 07:33:22: #2 finished! INFO @ Tue, 14 Jul 2020 07:33:22: #2 predicted fragment length is 236 bps INFO @ Tue, 14 Jul 2020 07:33:22: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 14 Jul 2020 07:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.20_model.r INFO @ Tue, 14 Jul 2020 07:33:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:33:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:33:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:33:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:33:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736458/SRX5736458.20_summits.bed INFO @ Tue, 14 Jul 2020 07:33:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1032 records, 4 fields): 3 millis CompletedMACS2peakCalling