Job ID = 6627045 SRX = SRX8325351 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:36:21 prefetch.2.10.7: 1) Downloading 'SRR11772157'... 2020-07-14T00:36:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:37:15 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:37:15 prefetch.2.10.7: 'SRR11772157' is valid 2020-07-14T00:37:15 prefetch.2.10.7: 1) 'SRR11772157' was downloaded successfully 2020-07-14T00:37:16 prefetch.2.10.7: 'SRR11772157' has 0 unresolved dependencies Read 2377376 spots for SRR11772157/SRR11772157.sra Written 2377376 spots for SRR11772157/SRR11772157.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627259 ("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: 00:07:00 2377376 reads; of these: 2377376 (100.00%) were paired; of these: 527252 (22.18%) aligned concordantly 0 times 1379021 (58.01%) aligned concordantly exactly 1 time 471103 (19.82%) aligned concordantly >1 times ---- 527252 pairs aligned concordantly 0 times; of these: 157755 (29.92%) aligned discordantly 1 time ---- 369497 pairs aligned 0 times concordantly or discordantly; of these: 738994 mates make up the pairs; of these: 386026 (52.24%) aligned 0 times 186184 (25.19%) aligned exactly 1 time 166784 (22.57%) aligned >1 times 91.88% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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_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] 709771 / 1906675 = 0.3723 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 09:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.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 09:46:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:46:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:47:00: 1000000 INFO @ Tue, 14 Jul 2020 09:47:08: 2000000 INFO @ Tue, 14 Jul 2020 09:47:16: #1 tag size is determined as 121 bps INFO @ Tue, 14 Jul 2020 09:47:16: #1 tag size = 121 INFO @ Tue, 14 Jul 2020 09:47:16: #1 total tags in treatment: 1187250 INFO @ Tue, 14 Jul 2020 09:47:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:47:16: #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 09:47:16: #1 tags after filtering in treatment: 1130640 INFO @ Tue, 14 Jul 2020 09:47:16: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:47:16: #1 finished! INFO @ Tue, 14 Jul 2020 09:47:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:47:16: #2 number of paired peaks: 285 WARNING @ Tue, 14 Jul 2020 09:47:16: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 14 Jul 2020 09:47:16: start model_add_line... INFO @ Tue, 14 Jul 2020 09:47:16: start X-correlation... INFO @ Tue, 14 Jul 2020 09:47:16: end of X-cor INFO @ Tue, 14 Jul 2020 09:47:16: #2 finished! INFO @ Tue, 14 Jul 2020 09:47:16: #2 predicted fragment length is 165 bps INFO @ Tue, 14 Jul 2020 09:47:16: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 14 Jul 2020 09:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.05_model.r WARNING @ Tue, 14 Jul 2020 09:47:16: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:47:16: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Tue, 14 Jul 2020 09:47:16: #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 09:47:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:47:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.05_summits.bed INFO @ Tue, 14 Jul 2020 09:47:20: Done! pass1 - making usageList (11 chroms): 11 millis pass2 - checking and writing primary data (241 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 09:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.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 09:47:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:47:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:47:30: 1000000 INFO @ Tue, 14 Jul 2020 09:47:38: 2000000 INFO @ Tue, 14 Jul 2020 09:47:46: #1 tag size is determined as 121 bps INFO @ Tue, 14 Jul 2020 09:47:46: #1 tag size = 121 INFO @ Tue, 14 Jul 2020 09:47:46: #1 total tags in treatment: 1187250 INFO @ Tue, 14 Jul 2020 09:47:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:47:46: #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 09:47:46: #1 tags after filtering in treatment: 1130640 INFO @ Tue, 14 Jul 2020 09:47:46: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:47:46: #1 finished! INFO @ Tue, 14 Jul 2020 09:47:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:47:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:47:46: #2 number of paired peaks: 285 WARNING @ Tue, 14 Jul 2020 09:47:46: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 14 Jul 2020 09:47:46: start model_add_line... INFO @ Tue, 14 Jul 2020 09:47:46: start X-correlation... INFO @ Tue, 14 Jul 2020 09:47:46: end of X-cor INFO @ Tue, 14 Jul 2020 09:47:46: #2 finished! INFO @ Tue, 14 Jul 2020 09:47:46: #2 predicted fragment length is 165 bps INFO @ Tue, 14 Jul 2020 09:47:46: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 14 Jul 2020 09:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.10_model.r WARNING @ Tue, 14 Jul 2020 09:47:46: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:47:46: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Tue, 14 Jul 2020 09:47:46: #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 09:47:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:47:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.10_summits.bed INFO @ Tue, 14 Jul 2020 09:47:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:47:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.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 09:47:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:47:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:48:00: 1000000 INFO @ Tue, 14 Jul 2020 09:48:08: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:48:17: #1 tag size is determined as 121 bps INFO @ Tue, 14 Jul 2020 09:48:17: #1 tag size = 121 INFO @ Tue, 14 Jul 2020 09:48:17: #1 total tags in treatment: 1187250 INFO @ Tue, 14 Jul 2020 09:48:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:48:17: #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 09:48:17: #1 tags after filtering in treatment: 1130640 INFO @ Tue, 14 Jul 2020 09:48:17: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:48:17: #1 finished! INFO @ Tue, 14 Jul 2020 09:48:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:48:17: #2 number of paired peaks: 285 WARNING @ Tue, 14 Jul 2020 09:48:17: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 14 Jul 2020 09:48:17: start model_add_line... INFO @ Tue, 14 Jul 2020 09:48:17: start X-correlation... INFO @ Tue, 14 Jul 2020 09:48:17: end of X-cor INFO @ Tue, 14 Jul 2020 09:48:17: #2 finished! INFO @ Tue, 14 Jul 2020 09:48:17: #2 predicted fragment length is 165 bps INFO @ Tue, 14 Jul 2020 09:48:17: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 14 Jul 2020 09:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.20_model.r WARNING @ Tue, 14 Jul 2020 09:48:17: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:48:17: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Tue, 14 Jul 2020 09:48:17: #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 09:48:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:48:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325351/SRX8325351.20_summits.bed INFO @ Tue, 14 Jul 2020 09:48:21: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 2 millis CompletedMACS2peakCalling