Job ID = 6626506 SRX = SRX5736484 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9508529 spots for SRR8956895/SRR8956895.sra Written 9508529 spots for SRR8956895/SRR8956895.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626675 ("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: 00:20:22 9508529 reads; of these: 9508529 (100.00%) were paired; of these: 1881119 (19.78%) aligned concordantly 0 times 5642631 (59.34%) aligned concordantly exactly 1 time 1984779 (20.87%) aligned concordantly >1 times ---- 1881119 pairs aligned concordantly 0 times; of these: 438734 (23.32%) aligned discordantly 1 time ---- 1442385 pairs aligned 0 times concordantly or discordantly; of these: 2884770 mates make up the pairs; of these: 2146796 (74.42%) aligned 0 times 360717 (12.50%) aligned exactly 1 time 377257 (13.08%) aligned >1 times 88.71% overall alignment rate Time searching: 00:20:22 Overall time: 00:20:22 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] 955421 / 8029727 = 0.1190 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 07:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.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 07:36:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:19: 1000000 INFO @ Tue, 14 Jul 2020 07:36:24: 2000000 INFO @ Tue, 14 Jul 2020 07:36:29: 3000000 INFO @ Tue, 14 Jul 2020 07:36:35: 4000000 INFO @ Tue, 14 Jul 2020 07:36:40: 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 07:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.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 07:36:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:45: 6000000 INFO @ Tue, 14 Jul 2020 07:36:49: 1000000 INFO @ Tue, 14 Jul 2020 07:36:51: 7000000 INFO @ Tue, 14 Jul 2020 07:36:55: 2000000 INFO @ Tue, 14 Jul 2020 07:36:57: 8000000 INFO @ Tue, 14 Jul 2020 07:37:00: 3000000 INFO @ Tue, 14 Jul 2020 07:37:02: 9000000 INFO @ Tue, 14 Jul 2020 07:37:06: 4000000 INFO @ Tue, 14 Jul 2020 07:37:08: 10000000 INFO @ Tue, 14 Jul 2020 07:37:12: 5000000 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 07:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.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 07:37:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:37:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:37:13: 11000000 INFO @ Tue, 14 Jul 2020 07:37:17: 6000000 INFO @ Tue, 14 Jul 2020 07:37:19: 12000000 INFO @ Tue, 14 Jul 2020 07:37:20: 1000000 INFO @ Tue, 14 Jul 2020 07:37:23: 7000000 INFO @ Tue, 14 Jul 2020 07:37:25: 13000000 INFO @ Tue, 14 Jul 2020 07:37:26: 2000000 INFO @ Tue, 14 Jul 2020 07:37:29: 8000000 INFO @ Tue, 14 Jul 2020 07:37:32: 3000000 INFO @ Tue, 14 Jul 2020 07:37:32: 14000000 INFO @ Tue, 14 Jul 2020 07:37:35: 9000000 INFO @ Tue, 14 Jul 2020 07:37:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:37:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:37:38: #1 total tags in treatment: 6720285 INFO @ Tue, 14 Jul 2020 07:37:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:38: #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 07:37:38: #1 tags after filtering in treatment: 6067012 INFO @ Tue, 14 Jul 2020 07:37:38: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:37:38: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:39: #2 number of paired peaks: 352 WARNING @ Tue, 14 Jul 2020 07:37:39: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 14 Jul 2020 07:37:39: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:39: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:39: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:39: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:39: #2 predicted fragment length is 144 bps INFO @ Tue, 14 Jul 2020 07:37:39: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 14 Jul 2020 07:37:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.05_model.r WARNING @ Tue, 14 Jul 2020 07:37:39: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:37:39: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 14 Jul 2020 07:37:39: #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 07:37:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:39: 4000000 INFO @ Tue, 14 Jul 2020 07:37:41: 10000000 INFO @ Tue, 14 Jul 2020 07:37:46: 5000000 INFO @ Tue, 14 Jul 2020 07:37:47: 11000000 INFO @ Tue, 14 Jul 2020 07:37:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:53: 6000000 INFO @ Tue, 14 Jul 2020 07:37:53: 12000000 INFO @ Tue, 14 Jul 2020 07:37:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.05_summits.bed INFO @ Tue, 14 Jul 2020 07:37:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2710 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:37:59: 13000000 INFO @ Tue, 14 Jul 2020 07:38:00: 7000000 INFO @ Tue, 14 Jul 2020 07:38:05: 14000000 INFO @ Tue, 14 Jul 2020 07:38:06: 8000000 INFO @ Tue, 14 Jul 2020 07:38:11: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:38:11: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:38:11: #1 total tags in treatment: 6720285 INFO @ Tue, 14 Jul 2020 07:38:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:38:11: #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 07:38:11: #1 tags after filtering in treatment: 6067012 INFO @ Tue, 14 Jul 2020 07:38:11: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:38:11: #1 finished! INFO @ Tue, 14 Jul 2020 07:38:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:38:11: #2 number of paired peaks: 352 WARNING @ Tue, 14 Jul 2020 07:38:11: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 14 Jul 2020 07:38:11: start model_add_line... INFO @ Tue, 14 Jul 2020 07:38:11: start X-correlation... INFO @ Tue, 14 Jul 2020 07:38:11: end of X-cor INFO @ Tue, 14 Jul 2020 07:38:11: #2 finished! INFO @ Tue, 14 Jul 2020 07:38:11: #2 predicted fragment length is 144 bps INFO @ Tue, 14 Jul 2020 07:38:11: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 14 Jul 2020 07:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.10_model.r WARNING @ Tue, 14 Jul 2020 07:38:11: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:38:11: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 14 Jul 2020 07:38:11: #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 07:38:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:38:13: 9000000 INFO @ Tue, 14 Jul 2020 07:38:20: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:38:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:38:27: 11000000 INFO @ Tue, 14 Jul 2020 07:38:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:38:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:38:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.10_summits.bed INFO @ Tue, 14 Jul 2020 07:38:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1157 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:38:33: 12000000 INFO @ Tue, 14 Jul 2020 07:38:40: 13000000 INFO @ Tue, 14 Jul 2020 07:38:46: 14000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:38:53: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:38:53: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:38:53: #1 total tags in treatment: 6720285 INFO @ Tue, 14 Jul 2020 07:38:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:38:53: #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 07:38:53: #1 tags after filtering in treatment: 6067012 INFO @ Tue, 14 Jul 2020 07:38:53: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:38:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:38:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:38:53: #2 number of paired peaks: 352 WARNING @ Tue, 14 Jul 2020 07:38:53: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 14 Jul 2020 07:38:53: start model_add_line... INFO @ Tue, 14 Jul 2020 07:38:53: start X-correlation... INFO @ Tue, 14 Jul 2020 07:38:53: end of X-cor INFO @ Tue, 14 Jul 2020 07:38:53: #2 finished! INFO @ Tue, 14 Jul 2020 07:38:53: #2 predicted fragment length is 144 bps INFO @ Tue, 14 Jul 2020 07:38:53: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 14 Jul 2020 07:38:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.20_model.r WARNING @ Tue, 14 Jul 2020 07:38:53: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:38:53: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 14 Jul 2020 07:38:53: #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 07:38:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:38:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:39:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736484/SRX5736484.20_summits.bed INFO @ Tue, 14 Jul 2020 07:39:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (537 records, 4 fields): 2 millis CompletedMACS2peakCalling