Job ID = 6458842 SRX = SRX5661488 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:42:55 prefetch.2.10.7: 1) Downloading 'SRR8874495'... 2020-06-21T12:42:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:51 prefetch.2.10.7: 1) 'SRR8874495' was downloaded successfully 2020-06-21T12:46:51 prefetch.2.10.7: 'SRR8874495' has 0 unresolved dependencies Read 32576945 spots for SRR8874495/SRR8874495.sra Written 32576945 spots for SRR8874495/SRR8874495.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: 00:09:49 32576945 reads; of these: 32576945 (100.00%) were unpaired; of these: 1221389 (3.75%) aligned 0 times 15116925 (46.40%) aligned exactly 1 time 16238631 (49.85%) aligned >1 times 96.25% overall alignment rate Time searching: 00:09:49 Overall time: 00:09:49 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 16 files... [bam_rmdupse_core] 10409910 / 31355556 = 0.3320 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 22:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.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 22:03:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:31: 1000000 INFO @ Sun, 21 Jun 2020 22:03:36: 2000000 INFO @ Sun, 21 Jun 2020 22:03:41: 3000000 INFO @ Sun, 21 Jun 2020 22:03:46: 4000000 INFO @ Sun, 21 Jun 2020 22:03:50: 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 22:03:55: 6000000 INFO @ Sun, 21 Jun 2020 22:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.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 22:03:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:00: 7000000 INFO @ Sun, 21 Jun 2020 22:04:03: 1000000 INFO @ Sun, 21 Jun 2020 22:04:05: 8000000 INFO @ Sun, 21 Jun 2020 22:04:09: 2000000 INFO @ Sun, 21 Jun 2020 22:04:11: 9000000 INFO @ Sun, 21 Jun 2020 22:04:15: 3000000 INFO @ Sun, 21 Jun 2020 22:04:16: 10000000 INFO @ Sun, 21 Jun 2020 22:04:21: 4000000 INFO @ Sun, 21 Jun 2020 22:04:21: 11000000 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 22:04:26: 12000000 INFO @ Sun, 21 Jun 2020 22:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.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 22:04:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:27: 5000000 INFO @ Sun, 21 Jun 2020 22:04:32: 13000000 INFO @ Sun, 21 Jun 2020 22:04:32: 1000000 INFO @ Sun, 21 Jun 2020 22:04:33: 6000000 INFO @ Sun, 21 Jun 2020 22:04:37: 14000000 INFO @ Sun, 21 Jun 2020 22:04:37: 2000000 INFO @ Sun, 21 Jun 2020 22:04:39: 7000000 INFO @ Sun, 21 Jun 2020 22:04:42: 15000000 INFO @ Sun, 21 Jun 2020 22:04:43: 3000000 INFO @ Sun, 21 Jun 2020 22:04:45: 8000000 INFO @ Sun, 21 Jun 2020 22:04:48: 16000000 INFO @ Sun, 21 Jun 2020 22:04:48: 4000000 INFO @ Sun, 21 Jun 2020 22:04:51: 9000000 INFO @ Sun, 21 Jun 2020 22:04:53: 17000000 INFO @ Sun, 21 Jun 2020 22:04:54: 5000000 INFO @ Sun, 21 Jun 2020 22:04:57: 10000000 INFO @ Sun, 21 Jun 2020 22:04:59: 18000000 INFO @ Sun, 21 Jun 2020 22:04:59: 6000000 INFO @ Sun, 21 Jun 2020 22:05:03: 11000000 INFO @ Sun, 21 Jun 2020 22:05:04: 19000000 INFO @ Sun, 21 Jun 2020 22:05:05: 7000000 INFO @ Sun, 21 Jun 2020 22:05:09: 12000000 INFO @ Sun, 21 Jun 2020 22:05:09: 20000000 INFO @ Sun, 21 Jun 2020 22:05:10: 8000000 INFO @ Sun, 21 Jun 2020 22:05:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:05:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:05:14: #1 total tags in treatment: 20945646 INFO @ Sun, 21 Jun 2020 22:05:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:14: #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 22:05:15: 13000000 INFO @ Sun, 21 Jun 2020 22:05:15: #1 tags after filtering in treatment: 20945604 INFO @ Sun, 21 Jun 2020 22:05:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:15: 9000000 INFO @ Sun, 21 Jun 2020 22:05:17: #2 number of paired peaks: 2429 INFO @ Sun, 21 Jun 2020 22:05:17: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:17: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:17: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:17: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:17: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:05:17: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 21 Jun 2020 22:05:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.05_model.r WARNING @ Sun, 21 Jun 2020 22:05:17: #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 22:05:17: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 21 Jun 2020 22:05:17: #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 22:05:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:20: 10000000 INFO @ Sun, 21 Jun 2020 22:05:21: 14000000 INFO @ Sun, 21 Jun 2020 22:05:26: 11000000 INFO @ Sun, 21 Jun 2020 22:05:27: 15000000 INFO @ Sun, 21 Jun 2020 22:05:31: 12000000 INFO @ Sun, 21 Jun 2020 22:05:33: 16000000 INFO @ Sun, 21 Jun 2020 22:05:36: 13000000 INFO @ Sun, 21 Jun 2020 22:05:39: 17000000 INFO @ Sun, 21 Jun 2020 22:05:41: 14000000 INFO @ Sun, 21 Jun 2020 22:05:45: 18000000 INFO @ Sun, 21 Jun 2020 22:05:47: 15000000 INFO @ Sun, 21 Jun 2020 22:05:51: 19000000 INFO @ Sun, 21 Jun 2020 22:05:52: 16000000 INFO @ Sun, 21 Jun 2020 22:05:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:57: 20000000 INFO @ Sun, 21 Jun 2020 22:05:57: 17000000 INFO @ Sun, 21 Jun 2020 22:06:03: 18000000 INFO @ Sun, 21 Jun 2020 22:06:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:03: #1 total tags in treatment: 20945646 INFO @ Sun, 21 Jun 2020 22:06:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:03: #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 22:06:03: #1 tags after filtering in treatment: 20945604 INFO @ Sun, 21 Jun 2020 22:06:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:05: #2 number of paired peaks: 2429 INFO @ Sun, 21 Jun 2020 22:06:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:05: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:06:05: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 21 Jun 2020 22:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.10_model.r WARNING @ Sun, 21 Jun 2020 22:06:05: #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 22:06:05: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 21 Jun 2020 22:06:05: #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 22:06:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:06:08: 19000000 INFO @ Sun, 21 Jun 2020 22:06:13: 20000000 INFO @ Sun, 21 Jun 2020 22:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.05_summits.bed INFO @ Sun, 21 Jun 2020 22:06:15: Done! pass1 - making usageList (994 chroms): 2 millis pass2 - checking and writing primary data (6764 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:06:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:06:18: #1 total tags in treatment: 20945646 INFO @ Sun, 21 Jun 2020 22:06:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:18: #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 22:06:18: #1 tags after filtering in treatment: 20945604 INFO @ Sun, 21 Jun 2020 22:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:20: #2 number of paired peaks: 2429 INFO @ Sun, 21 Jun 2020 22:06:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:20: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:06:20: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 21 Jun 2020 22:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.20_model.r WARNING @ Sun, 21 Jun 2020 22:06:20: #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 22:06:20: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 21 Jun 2020 22:06:20: #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 22:06:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.10_summits.bed INFO @ Sun, 21 Jun 2020 22:07:01: Done! pass1 - making usageList (825 chroms): 2 millis pass2 - checking and writing primary data (3547 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661488/SRX5661488.20_summits.bed INFO @ Sun, 21 Jun 2020 22:07:19: Done! pass1 - making usageList (641 chroms): 2 millis pass2 - checking and writing primary data (2277 records, 4 fields): 20 millis CompletedMACS2peakCalling