Job ID = 6627012 SRX = SRX8325344 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6628138 spots for SRR11772150/SRR11772150.sra Written 6628138 spots for SRR11772150/SRR11772150.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627264 ("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: 00:22:31 6628138 reads; of these: 6628138 (100.00%) were paired; of these: 1784815 (26.93%) aligned concordantly 0 times 3531258 (53.28%) aligned concordantly exactly 1 time 1312065 (19.80%) aligned concordantly >1 times ---- 1784815 pairs aligned concordantly 0 times; of these: 576347 (32.29%) aligned discordantly 1 time ---- 1208468 pairs aligned 0 times concordantly or discordantly; of these: 2416936 mates make up the pairs; of these: 1172692 (48.52%) aligned 0 times 590505 (24.43%) aligned exactly 1 time 653739 (27.05%) aligned >1 times 91.15% overall alignment rate Time searching: 00:22:31 Overall time: 00:22:31 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] 2240390 / 5214426 = 0.4297 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 09:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.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 09:51:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:51:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:16: 1000000 INFO @ Tue, 14 Jul 2020 09:51:23: 2000000 INFO @ Tue, 14 Jul 2020 09:51:31: 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 09:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.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 09:51:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:51:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:39: 4000000 INFO @ Tue, 14 Jul 2020 09:51:45: 1000000 INFO @ Tue, 14 Jul 2020 09:51:47: 5000000 INFO @ Tue, 14 Jul 2020 09:51:52: 2000000 INFO @ Tue, 14 Jul 2020 09:51:55: 6000000 INFO @ Tue, 14 Jul 2020 09:51:59: 3000000 INFO @ Tue, 14 Jul 2020 09:52:04: 7000000 BedGraph に変換中... INFO @ Tue, 14 Jul 2020 09:52:06: 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 09:52:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.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 09:52:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:52:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:52:08: #1 tag size is determined as 117 bps INFO @ Tue, 14 Jul 2020 09:52:08: #1 tag size = 117 INFO @ Tue, 14 Jul 2020 09:52:08: #1 total tags in treatment: 2802874 INFO @ Tue, 14 Jul 2020 09:52:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:52:08: #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 09:52:09: #1 tags after filtering in treatment: 2569185 INFO @ Tue, 14 Jul 2020 09:52:09: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 09:52:09: #1 finished! INFO @ Tue, 14 Jul 2020 09:52:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:52:09: #2 number of paired peaks: 560 WARNING @ Tue, 14 Jul 2020 09:52:09: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Tue, 14 Jul 2020 09:52:09: start model_add_line... INFO @ Tue, 14 Jul 2020 09:52:09: start X-correlation... INFO @ Tue, 14 Jul 2020 09:52:09: end of X-cor INFO @ Tue, 14 Jul 2020 09:52:09: #2 finished! INFO @ Tue, 14 Jul 2020 09:52:09: #2 predicted fragment length is 173 bps INFO @ Tue, 14 Jul 2020 09:52:09: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 14 Jul 2020 09:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.05_model.r WARNING @ Tue, 14 Jul 2020 09:52:09: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:52:09: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 14 Jul 2020 09:52:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:52:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:52:13: 5000000 INFO @ Tue, 14 Jul 2020 09:52:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:52:17: 1000000 INFO @ Tue, 14 Jul 2020 09:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.05_summits.bed INFO @ Tue, 14 Jul 2020 09:52:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1674 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:52:20: 6000000 INFO @ Tue, 14 Jul 2020 09:52:25: 2000000 INFO @ Tue, 14 Jul 2020 09:52:27: 7000000 INFO @ Tue, 14 Jul 2020 09:52:32: #1 tag size is determined as 117 bps INFO @ Tue, 14 Jul 2020 09:52:32: #1 tag size = 117 INFO @ Tue, 14 Jul 2020 09:52:32: #1 total tags in treatment: 2802874 INFO @ Tue, 14 Jul 2020 09:52:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:52:32: #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 09:52:32: #1 tags after filtering in treatment: 2569185 INFO @ Tue, 14 Jul 2020 09:52:32: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 09:52:32: #1 finished! INFO @ Tue, 14 Jul 2020 09:52:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:52:32: #2 number of paired peaks: 560 WARNING @ Tue, 14 Jul 2020 09:52:32: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Tue, 14 Jul 2020 09:52:32: start model_add_line... INFO @ Tue, 14 Jul 2020 09:52:32: start X-correlation... INFO @ Tue, 14 Jul 2020 09:52:32: end of X-cor INFO @ Tue, 14 Jul 2020 09:52:32: #2 finished! INFO @ Tue, 14 Jul 2020 09:52:32: #2 predicted fragment length is 173 bps INFO @ Tue, 14 Jul 2020 09:52:32: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 14 Jul 2020 09:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.10_model.r WARNING @ Tue, 14 Jul 2020 09:52:32: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:52:32: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 14 Jul 2020 09:52:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:52:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:52:34: 3000000 INFO @ Tue, 14 Jul 2020 09:52:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.10_summits.bed INFO @ Tue, 14 Jul 2020 09:52:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:52:42: 4000000 INFO @ Tue, 14 Jul 2020 09:52:50: 5000000 INFO @ Tue, 14 Jul 2020 09:52:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:53:07: 7000000 INFO @ Tue, 14 Jul 2020 09:53:12: #1 tag size is determined as 117 bps INFO @ Tue, 14 Jul 2020 09:53:12: #1 tag size = 117 INFO @ Tue, 14 Jul 2020 09:53:12: #1 total tags in treatment: 2802874 INFO @ Tue, 14 Jul 2020 09:53:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:53:12: #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 09:53:12: #1 tags after filtering in treatment: 2569185 INFO @ Tue, 14 Jul 2020 09:53:12: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 09:53:12: #1 finished! INFO @ Tue, 14 Jul 2020 09:53:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:53:12: #2 number of paired peaks: 560 WARNING @ Tue, 14 Jul 2020 09:53:12: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Tue, 14 Jul 2020 09:53:12: start model_add_line... INFO @ Tue, 14 Jul 2020 09:53:12: start X-correlation... INFO @ Tue, 14 Jul 2020 09:53:12: end of X-cor INFO @ Tue, 14 Jul 2020 09:53:12: #2 finished! INFO @ Tue, 14 Jul 2020 09:53:12: #2 predicted fragment length is 173 bps INFO @ Tue, 14 Jul 2020 09:53:12: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 14 Jul 2020 09:53:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.20_model.r WARNING @ Tue, 14 Jul 2020 09:53:12: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:53:12: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 14 Jul 2020 09:53:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:53:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:53:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:53:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:53:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:53:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:53:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325344/SRX8325344.20_summits.bed INFO @ Tue, 14 Jul 2020 09:53:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 1 millis CompletedMACS2peakCalling