Job ID = 6627578 SRX = SRX8521412 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:04:08 prefetch.2.10.7: 1) Downloading 'SRR11978390'... 2020-07-14T03:04:08 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:09:22 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:09:22 prefetch.2.10.7: 'SRR11978390' is valid 2020-07-14T03:09:22 prefetch.2.10.7: 1) 'SRR11978390' was downloaded successfully 2020-07-14T03:09:22 prefetch.2.10.7: 'SRR11978390' has 0 unresolved dependencies Read 12811185 spots for SRR11978390/SRR11978390.sra Written 12811185 spots for SRR11978390/SRR11978390.sra 2020-07-14T03:10:18 prefetch.2.10.7: 1) Downloading 'SRR11978391'... 2020-07-14T03:10:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:11:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:11:42 prefetch.2.10.7: 'SRR11978391' is valid 2020-07-14T03:11:42 prefetch.2.10.7: 1) 'SRR11978391' was downloaded successfully 2020-07-14T03:11:42 prefetch.2.10.7: 'SRR11978391' has 0 unresolved dependencies Read 12544846 spots for SRR11978391/SRR11978391.sra Written 12544846 spots for SRR11978391/SRR11978391.sra 2020-07-14T03:12:37 prefetch.2.10.7: 1) Downloading 'SRR11978392'... 2020-07-14T03:12:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:14:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:14:04 prefetch.2.10.7: 'SRR11978392' is valid 2020-07-14T03:14:04 prefetch.2.10.7: 1) 'SRR11978392' was downloaded successfully 2020-07-14T03:14:04 prefetch.2.10.7: 'SRR11978392' has 0 unresolved dependencies Read 12742368 spots for SRR11978392/SRR11978392.sra Written 12742368 spots for SRR11978392/SRR11978392.sra 2020-07-14T03:15:16 prefetch.2.10.7: 1) Downloading 'SRR11978393'... 2020-07-14T03:15:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:23:18 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:23:19 prefetch.2.10.7: 'SRR11978393' is valid 2020-07-14T03:23:19 prefetch.2.10.7: 1) 'SRR11978393' was downloaded successfully 2020-07-14T03:23:19 prefetch.2.10.7: 'SRR11978393' has 0 unresolved dependencies Read 12537783 spots for SRR11978393/SRR11978393.sra Written 12537783 spots for SRR11978393/SRR11978393.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627799 ("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: 00:06:26 50636182 reads; of these: 50636182 (100.00%) were unpaired; of these: 47244735 (93.30%) aligned 0 times 2575087 (5.09%) aligned exactly 1 time 816360 (1.61%) aligned >1 times 6.70% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 704876 / 3391447 = 0.2078 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 12:32:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.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 12:32:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:32:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:32:15: 1000000 INFO @ Tue, 14 Jul 2020 12:32:20: 2000000 INFO @ Tue, 14 Jul 2020 12:32:24: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:32:24: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:32:24: #1 total tags in treatment: 2686571 INFO @ Tue, 14 Jul 2020 12:32:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:32:24: #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 12:32:24: #1 tags after filtering in treatment: 2686571 INFO @ Tue, 14 Jul 2020 12:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:32:24: #1 finished! INFO @ Tue, 14 Jul 2020 12:32:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:32:24: #2 number of paired peaks: 665 WARNING @ Tue, 14 Jul 2020 12:32:24: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 14 Jul 2020 12:32:24: start model_add_line... INFO @ Tue, 14 Jul 2020 12:32:24: start X-correlation... INFO @ Tue, 14 Jul 2020 12:32:24: end of X-cor INFO @ Tue, 14 Jul 2020 12:32:24: #2 finished! INFO @ Tue, 14 Jul 2020 12:32:24: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:32:24: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 12:32:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.05_model.r WARNING @ Tue, 14 Jul 2020 12:32:24: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:32:24: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 12:32:24: #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 12:32:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:32:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:32:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.05_summits.bed INFO @ Tue, 14 Jul 2020 12:32:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1322 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 12:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.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 12:32:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:32:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:32:45: 1000000 INFO @ Tue, 14 Jul 2020 12:32:51: 2000000 INFO @ Tue, 14 Jul 2020 12:32:54: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:32:54: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:32:54: #1 total tags in treatment: 2686571 INFO @ Tue, 14 Jul 2020 12:32:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:32:54: #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 12:32:54: #1 tags after filtering in treatment: 2686571 INFO @ Tue, 14 Jul 2020 12:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:32:54: #1 finished! INFO @ Tue, 14 Jul 2020 12:32:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:32:54: #2 number of paired peaks: 665 WARNING @ Tue, 14 Jul 2020 12:32:54: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 14 Jul 2020 12:32:54: start model_add_line... INFO @ Tue, 14 Jul 2020 12:32:54: start X-correlation... INFO @ Tue, 14 Jul 2020 12:32:54: end of X-cor INFO @ Tue, 14 Jul 2020 12:32:54: #2 finished! INFO @ Tue, 14 Jul 2020 12:32:54: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:32:54: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 12:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.10_model.r WARNING @ Tue, 14 Jul 2020 12:32:54: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:32:54: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 12:32:54: #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 12:32:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:33:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.10_summits.bed INFO @ Tue, 14 Jul 2020 12:33:03: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (549 records, 4 fields): 2 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 12:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.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 12:33:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:33:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:33:15: 1000000 INFO @ Tue, 14 Jul 2020 12:33:21: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:33:24: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:33:24: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:33:24: #1 total tags in treatment: 2686571 INFO @ Tue, 14 Jul 2020 12:33:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:33:24: #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 12:33:24: #1 tags after filtering in treatment: 2686571 INFO @ Tue, 14 Jul 2020 12:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:33:24: #1 finished! INFO @ Tue, 14 Jul 2020 12:33:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:33:25: #2 number of paired peaks: 665 WARNING @ Tue, 14 Jul 2020 12:33:25: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 14 Jul 2020 12:33:25: start model_add_line... INFO @ Tue, 14 Jul 2020 12:33:25: start X-correlation... INFO @ Tue, 14 Jul 2020 12:33:25: end of X-cor INFO @ Tue, 14 Jul 2020 12:33:25: #2 finished! INFO @ Tue, 14 Jul 2020 12:33:25: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:33:25: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 12:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.20_model.r WARNING @ Tue, 14 Jul 2020 12:33:25: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:33:25: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 12:33:25: #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 12:33:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:33:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:33:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521412/SRX8521412.20_summits.bed INFO @ Tue, 14 Jul 2020 12:33:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling