Job ID = 6627450 SRX = SRX8521384 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:32:32 prefetch.2.10.7: 1) Downloading 'SRR11978278'... 2020-07-14T02:32:32 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:34:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:34:39 prefetch.2.10.7: 'SRR11978278' is valid 2020-07-14T02:34:39 prefetch.2.10.7: 1) 'SRR11978278' was downloaded successfully 2020-07-14T02:34:39 prefetch.2.10.7: 'SRR11978278' has 0 unresolved dependencies Read 11703929 spots for SRR11978278/SRR11978278.sra Written 11703929 spots for SRR11978278/SRR11978278.sra 2020-07-14T02:35:27 prefetch.2.10.7: 1) Downloading 'SRR11978279'... 2020-07-14T02:35:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:50:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:50:24 prefetch.2.10.7: 'SRR11978279' is valid 2020-07-14T02:50:24 prefetch.2.10.7: 1) 'SRR11978279' was downloaded successfully 2020-07-14T02:50:24 prefetch.2.10.7: 'SRR11978279' has 0 unresolved dependencies Read 11628310 spots for SRR11978279/SRR11978279.sra Written 11628310 spots for SRR11978279/SRR11978279.sra 2020-07-14T02:51:17 prefetch.2.10.7: 1) Downloading 'SRR11978280'... 2020-07-14T02:51:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:52:21 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:52:22 prefetch.2.10.7: 'SRR11978280' is valid 2020-07-14T02:52:22 prefetch.2.10.7: 1) 'SRR11978280' was downloaded successfully 2020-07-14T02:52:22 prefetch.2.10.7: 'SRR11978280' has 0 unresolved dependencies Read 11558580 spots for SRR11978280/SRR11978280.sra Written 11558580 spots for SRR11978280/SRR11978280.sra 2020-07-14T02:53:15 prefetch.2.10.7: 1) Downloading 'SRR11978281'... 2020-07-14T02:53:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:54:45 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:54:46 prefetch.2.10.7: 'SRR11978281' is valid 2020-07-14T02:54:46 prefetch.2.10.7: 1) 'SRR11978281' was downloaded successfully 2020-07-14T02:54:46 prefetch.2.10.7: 'SRR11978281' has 0 unresolved dependencies Read 11682259 spots for SRR11978281/SRR11978281.sra Written 11682259 spots for SRR11978281/SRR11978281.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627693 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:32 46573078 reads; of these: 46573078 (100.00%) were unpaired; of these: 42236352 (90.69%) aligned 0 times 3208868 (6.89%) aligned exactly 1 time 1127858 (2.42%) aligned >1 times 9.31% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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] 831896 / 4336726 = 0.1918 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 12:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.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 12:03:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:03:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:03:58: 1000000 INFO @ Tue, 14 Jul 2020 12:04:03: 2000000 INFO @ Tue, 14 Jul 2020 12:04:09: 3000000 INFO @ Tue, 14 Jul 2020 12:04:11: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 12:04:11: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 12:04:11: #1 total tags in treatment: 3504830 INFO @ Tue, 14 Jul 2020 12:04:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:04:11: #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 12:04:11: #1 tags after filtering in treatment: 3504830 INFO @ Tue, 14 Jul 2020 12:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:04:11: #1 finished! INFO @ Tue, 14 Jul 2020 12:04:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:04:12: #2 number of paired peaks: 650 WARNING @ Tue, 14 Jul 2020 12:04:12: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Tue, 14 Jul 2020 12:04:12: start model_add_line... INFO @ Tue, 14 Jul 2020 12:04:12: start X-correlation... INFO @ Tue, 14 Jul 2020 12:04:12: end of X-cor INFO @ Tue, 14 Jul 2020 12:04:12: #2 finished! INFO @ Tue, 14 Jul 2020 12:04:12: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:04:12: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.05_model.r WARNING @ Tue, 14 Jul 2020 12:04:12: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:04:12: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:04:12: #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 12:04:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:04:19: #3 Call peaks for each chromosome... 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 12:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.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 12:04:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:04:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:04:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.05_summits.bed INFO @ Tue, 14 Jul 2020 12:04:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1623 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:04:29: 1000000 INFO @ Tue, 14 Jul 2020 12:04:35: 2000000 INFO @ Tue, 14 Jul 2020 12:04:40: 3000000 INFO @ Tue, 14 Jul 2020 12:04:43: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 12:04:43: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 12:04:43: #1 total tags in treatment: 3504830 INFO @ Tue, 14 Jul 2020 12:04:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:04:43: #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 12:04:43: #1 tags after filtering in treatment: 3504830 INFO @ Tue, 14 Jul 2020 12:04:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:04:43: #1 finished! INFO @ Tue, 14 Jul 2020 12:04:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:04:43: #2 number of paired peaks: 650 WARNING @ Tue, 14 Jul 2020 12:04:43: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Tue, 14 Jul 2020 12:04:43: start model_add_line... INFO @ Tue, 14 Jul 2020 12:04:43: start X-correlation... INFO @ Tue, 14 Jul 2020 12:04:43: end of X-cor INFO @ Tue, 14 Jul 2020 12:04:43: #2 finished! INFO @ Tue, 14 Jul 2020 12:04:43: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:04:43: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:04:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.10_model.r WARNING @ Tue, 14 Jul 2020 12:04:43: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:04:43: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:04:43: #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 12:04:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:04:43: #3 Pre-compute pvalue-qvalue table... 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 12:04:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.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 12:04:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.10_summits.bed INFO @ Tue, 14 Jul 2020 12:04:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (730 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:04:58: 1000000 INFO @ Tue, 14 Jul 2020 12:05:03: 2000000 INFO @ Tue, 14 Jul 2020 12:05:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:05:12: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 12:05:12: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 12:05:12: #1 total tags in treatment: 3504830 INFO @ Tue, 14 Jul 2020 12:05:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:12: #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 12:05:12: #1 tags after filtering in treatment: 3504830 INFO @ Tue, 14 Jul 2020 12:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:12: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:12: #2 number of paired peaks: 650 WARNING @ Tue, 14 Jul 2020 12:05:12: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:12: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:12: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:12: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:12: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:12: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:05:12: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.20_model.r WARNING @ Tue, 14 Jul 2020 12:05:12: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:12: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:05:12: #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 12:05:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:05:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:05:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521384/SRX8521384.20_summits.bed INFO @ Tue, 14 Jul 2020 12:05:23: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling