Job ID = 6458970 SRX = SRX5827838 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:01:35 prefetch.2.10.7: 1) Downloading 'SRR9051589'... 2020-06-21T13:01:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:06:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:06:02 prefetch.2.10.7: 1) 'SRR9051589' was downloaded successfully 2020-06-21T13:06:02 prefetch.2.10.7: 'SRR9051589' has 0 unresolved dependencies Read 30051912 spots for SRR9051589/SRR9051589.sra Written 30051912 spots for SRR9051589/SRR9051589.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:41 30051912 reads; of these: 30051912 (100.00%) were unpaired; of these: 5211567 (17.34%) aligned 0 times 19157243 (63.75%) aligned exactly 1 time 5683102 (18.91%) aligned >1 times 82.66% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14251769 / 24840345 = 0.5737 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 @ Sun, 21 Jun 2020 22:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.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 @ Sun, 21 Jun 2020 22:21:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:11: 1000000 INFO @ Sun, 21 Jun 2020 22:21:16: 2000000 INFO @ Sun, 21 Jun 2020 22:21:20: 3000000 INFO @ Sun, 21 Jun 2020 22:21:25: 4000000 INFO @ Sun, 21 Jun 2020 22:21:30: 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 @ Sun, 21 Jun 2020 22:21:35: 6000000 INFO @ Sun, 21 Jun 2020 22:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.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 @ Sun, 21 Jun 2020 22:21:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:40: 7000000 INFO @ Sun, 21 Jun 2020 22:21:41: 1000000 INFO @ Sun, 21 Jun 2020 22:21:45: 8000000 INFO @ Sun, 21 Jun 2020 22:21:46: 2000000 INFO @ Sun, 21 Jun 2020 22:21:51: 9000000 INFO @ Sun, 21 Jun 2020 22:21:52: 3000000 INFO @ Sun, 21 Jun 2020 22:21:57: 10000000 INFO @ Sun, 21 Jun 2020 22:21:57: 4000000 INFO @ Sun, 21 Jun 2020 22:22:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:22:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:22:00: #1 total tags in treatment: 10588576 INFO @ Sun, 21 Jun 2020 22:22:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:22:00: #1 tags after filtering in treatment: 10588575 INFO @ Sun, 21 Jun 2020 22:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:01: #2 number of paired peaks: 1001 INFO @ Sun, 21 Jun 2020 22:22:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:01: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:22:01: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 22:22:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.05_model.r WARNING @ Sun, 21 Jun 2020 22:22:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:01: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 22:22:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:22:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:02: 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 @ Sun, 21 Jun 2020 22:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.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 @ Sun, 21 Jun 2020 22:22:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:22:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:22:07: 6000000 INFO @ Sun, 21 Jun 2020 22:22:10: 1000000 INFO @ Sun, 21 Jun 2020 22:22:13: 7000000 INFO @ Sun, 21 Jun 2020 22:22:16: 2000000 INFO @ Sun, 21 Jun 2020 22:22:18: 8000000 INFO @ Sun, 21 Jun 2020 22:22:21: 3000000 INFO @ Sun, 21 Jun 2020 22:22:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:24: 9000000 INFO @ Sun, 21 Jun 2020 22:22:27: 4000000 INFO @ Sun, 21 Jun 2020 22:22:29: 10000000 INFO @ Sun, 21 Jun 2020 22:22:32: 5000000 INFO @ Sun, 21 Jun 2020 22:22:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:22:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:22:33: #1 total tags in treatment: 10588576 INFO @ Sun, 21 Jun 2020 22:22:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:22:33: #1 tags after filtering in treatment: 10588575 INFO @ Sun, 21 Jun 2020 22:22:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:34: #2 number of paired peaks: 1001 INFO @ Sun, 21 Jun 2020 22:22:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:34: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:22:34: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 22:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.10_model.r WARNING @ Sun, 21 Jun 2020 22:22:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:34: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 22:22:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:22:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:36: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (2930 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:22:37: 6000000 INFO @ Sun, 21 Jun 2020 22:22:43: 7000000 INFO @ Sun, 21 Jun 2020 22:22:48: 8000000 INFO @ Sun, 21 Jun 2020 22:22:53: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:22:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:59: 10000000 INFO @ Sun, 21 Jun 2020 22:23:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:02: #1 total tags in treatment: 10588576 INFO @ Sun, 21 Jun 2020 22:23:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:23:03: #1 tags after filtering in treatment: 10588575 INFO @ Sun, 21 Jun 2020 22:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:03: #2 number of paired peaks: 1001 INFO @ Sun, 21 Jun 2020 22:23:03: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:04: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:23:04: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 22:23:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.20_model.r WARNING @ Sun, 21 Jun 2020 22:23:04: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:04: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 22:23:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:23:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:09: Done! pass1 - making usageList (548 chroms): 2 millis pass2 - checking and writing primary data (2017 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:23:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827838/SRX5827838.20_summits.bed INFO @ Sun, 21 Jun 2020 22:23:39: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 12 millis CompletedMACS2peakCalling