Job ID = 6626459 SRX = SRX1532035 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9079503 spots for SRR3103385/SRR3103385.sra Written 9079503 spots for SRR3103385/SRR3103385.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626593 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:41 9079503 reads; of these: 9079503 (100.00%) were unpaired; of these: 515169 (5.67%) aligned 0 times 5977573 (65.84%) aligned exactly 1 time 2586761 (28.49%) aligned >1 times 94.33% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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_rmdupse_core] 496242 / 8564334 = 0.0579 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 07:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.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 07:08:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:08:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:09:00: 1000000 INFO @ Tue, 14 Jul 2020 07:09:06: 2000000 INFO @ Tue, 14 Jul 2020 07:09:12: 3000000 INFO @ Tue, 14 Jul 2020 07:09:18: 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 07:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.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 07:09:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:09:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:09:24: 5000000 INFO @ Tue, 14 Jul 2020 07:09:30: 1000000 INFO @ Tue, 14 Jul 2020 07:09:31: 6000000 INFO @ Tue, 14 Jul 2020 07:09:36: 2000000 INFO @ Tue, 14 Jul 2020 07:09:37: 7000000 INFO @ Tue, 14 Jul 2020 07:09:42: 3000000 INFO @ Tue, 14 Jul 2020 07:09:43: 8000000 INFO @ Tue, 14 Jul 2020 07:09:44: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:09:44: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:09:44: #1 total tags in treatment: 8068092 INFO @ Tue, 14 Jul 2020 07:09:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:09:44: #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 07:09:44: #1 tags after filtering in treatment: 8068092 INFO @ Tue, 14 Jul 2020 07:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:09:44: #1 finished! INFO @ Tue, 14 Jul 2020 07:09:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:09:45: #2 number of paired peaks: 929 WARNING @ Tue, 14 Jul 2020 07:09:45: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Tue, 14 Jul 2020 07:09:45: start model_add_line... INFO @ Tue, 14 Jul 2020 07:09:45: start X-correlation... INFO @ Tue, 14 Jul 2020 07:09:45: end of X-cor INFO @ Tue, 14 Jul 2020 07:09:45: #2 finished! INFO @ Tue, 14 Jul 2020 07:09:45: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 07:09:45: #2 alternative fragment length(s) may be 4,60 bps INFO @ Tue, 14 Jul 2020 07:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.05_model.r WARNING @ Tue, 14 Jul 2020 07:09:45: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:09:45: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Tue, 14 Jul 2020 07:09:45: #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 07:09:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:09:48: 4000000 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 07:09:54: 5000000 INFO @ Tue, 14 Jul 2020 07:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.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 07:09:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:09:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:09:59: 1000000 INFO @ Tue, 14 Jul 2020 07:10:00: 6000000 INFO @ Tue, 14 Jul 2020 07:10:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:10:05: 2000000 INFO @ Tue, 14 Jul 2020 07:10:06: 7000000 INFO @ Tue, 14 Jul 2020 07:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.05_summits.bed INFO @ Tue, 14 Jul 2020 07:10:09: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2611 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:10:11: 3000000 INFO @ Tue, 14 Jul 2020 07:10:12: 8000000 INFO @ Tue, 14 Jul 2020 07:10:12: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:10:12: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:10:12: #1 total tags in treatment: 8068092 INFO @ Tue, 14 Jul 2020 07:10:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:10:12: #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 07:10:12: #1 tags after filtering in treatment: 8068092 INFO @ Tue, 14 Jul 2020 07:10:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:10:12: #1 finished! INFO @ Tue, 14 Jul 2020 07:10:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:10:13: #2 number of paired peaks: 929 WARNING @ Tue, 14 Jul 2020 07:10:13: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Tue, 14 Jul 2020 07:10:13: start model_add_line... INFO @ Tue, 14 Jul 2020 07:10:13: start X-correlation... INFO @ Tue, 14 Jul 2020 07:10:13: end of X-cor INFO @ Tue, 14 Jul 2020 07:10:13: #2 finished! INFO @ Tue, 14 Jul 2020 07:10:13: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 07:10:13: #2 alternative fragment length(s) may be 4,60 bps INFO @ Tue, 14 Jul 2020 07:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.10_model.r WARNING @ Tue, 14 Jul 2020 07:10:13: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:10:13: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Tue, 14 Jul 2020 07:10:13: #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 07:10:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:10:16: 4000000 INFO @ Tue, 14 Jul 2020 07:10:22: 5000000 INFO @ Tue, 14 Jul 2020 07:10:27: 6000000 INFO @ Tue, 14 Jul 2020 07:10:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:10:33: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.10_summits.bed INFO @ Tue, 14 Jul 2020 07:10:38: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1406 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:10:38: 8000000 INFO @ Tue, 14 Jul 2020 07:10:38: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:10:38: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:10:38: #1 total tags in treatment: 8068092 INFO @ Tue, 14 Jul 2020 07:10:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:10:38: #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 07:10:38: #1 tags after filtering in treatment: 8068092 INFO @ Tue, 14 Jul 2020 07:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:10:38: #1 finished! INFO @ Tue, 14 Jul 2020 07:10:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:10:39: #2 number of paired peaks: 929 WARNING @ Tue, 14 Jul 2020 07:10:39: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Tue, 14 Jul 2020 07:10:39: start model_add_line... INFO @ Tue, 14 Jul 2020 07:10:39: start X-correlation... INFO @ Tue, 14 Jul 2020 07:10:39: end of X-cor INFO @ Tue, 14 Jul 2020 07:10:39: #2 finished! INFO @ Tue, 14 Jul 2020 07:10:39: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 07:10:39: #2 alternative fragment length(s) may be 4,60 bps INFO @ Tue, 14 Jul 2020 07:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.20_model.r WARNING @ Tue, 14 Jul 2020 07:10:39: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:10:39: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Tue, 14 Jul 2020 07:10:39: #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 07:10:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:10:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:10:55: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:11:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:11:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:11:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532035/SRX1532035.20_summits.bed INFO @ Tue, 14 Jul 2020 07:11:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 12 millis CompletedMACS2peakCalling