Job ID = 6528100 SRX = SRX4664657 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:14:50 prefetch.2.10.7: 1) Downloading 'SRR7813084'... 2020-06-29T14:14:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:17:06 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:17:06 prefetch.2.10.7: 1) 'SRR7813084' was downloaded successfully Read 33736632 spots for SRR7813084/SRR7813084.sra Written 33736632 spots for SRR7813084/SRR7813084.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: 00:12:27 33736632 reads; of these: 33736632 (100.00%) were unpaired; of these: 827875 (2.45%) aligned 0 times 21850367 (64.77%) aligned exactly 1 time 11058390 (32.78%) aligned >1 times 97.55% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 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_sort_core] merging from 16 files... [bam_rmdupse_core] 5847423 / 32908757 = 0.1777 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 @ Mon, 29 Jun 2020 23:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.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 @ Mon, 29 Jun 2020 23:44:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:44:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:44:35: 1000000 INFO @ Mon, 29 Jun 2020 23:44:40: 2000000 INFO @ Mon, 29 Jun 2020 23:44:45: 3000000 INFO @ Mon, 29 Jun 2020 23:44:51: 4000000 INFO @ Mon, 29 Jun 2020 23:44:56: 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 @ Mon, 29 Jun 2020 23:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.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 @ Mon, 29 Jun 2020 23:45:00: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:45:00: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:45:02: 6000000 INFO @ Mon, 29 Jun 2020 23:45:07: 1000000 INFO @ Mon, 29 Jun 2020 23:45:08: 7000000 INFO @ Mon, 29 Jun 2020 23:45:14: 2000000 INFO @ Mon, 29 Jun 2020 23:45:14: 8000000 INFO @ Mon, 29 Jun 2020 23:45:21: 9000000 INFO @ Mon, 29 Jun 2020 23:45:22: 3000000 INFO @ Mon, 29 Jun 2020 23:45:27: 10000000 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 @ Mon, 29 Jun 2020 23:45:29: 4000000 INFO @ Mon, 29 Jun 2020 23:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.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 @ Mon, 29 Jun 2020 23:45:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:45:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:45:34: 11000000 INFO @ Mon, 29 Jun 2020 23:45:36: 5000000 INFO @ Mon, 29 Jun 2020 23:45:37: 1000000 INFO @ Mon, 29 Jun 2020 23:45:40: 12000000 INFO @ Mon, 29 Jun 2020 23:45:43: 6000000 INFO @ Mon, 29 Jun 2020 23:45:45: 2000000 INFO @ Mon, 29 Jun 2020 23:45:46: 13000000 INFO @ Mon, 29 Jun 2020 23:45:50: 7000000 INFO @ Mon, 29 Jun 2020 23:45:52: 3000000 INFO @ Mon, 29 Jun 2020 23:45:53: 14000000 INFO @ Mon, 29 Jun 2020 23:45:57: 8000000 INFO @ Mon, 29 Jun 2020 23:45:59: 4000000 INFO @ Mon, 29 Jun 2020 23:45:59: 15000000 INFO @ Mon, 29 Jun 2020 23:46:04: 9000000 INFO @ Mon, 29 Jun 2020 23:46:05: 16000000 INFO @ Mon, 29 Jun 2020 23:46:06: 5000000 INFO @ Mon, 29 Jun 2020 23:46:11: 10000000 INFO @ Mon, 29 Jun 2020 23:46:12: 17000000 INFO @ Mon, 29 Jun 2020 23:46:13: 6000000 INFO @ Mon, 29 Jun 2020 23:46:18: 11000000 INFO @ Mon, 29 Jun 2020 23:46:18: 18000000 INFO @ Mon, 29 Jun 2020 23:46:20: 7000000 INFO @ Mon, 29 Jun 2020 23:46:24: 19000000 INFO @ Mon, 29 Jun 2020 23:46:25: 12000000 INFO @ Mon, 29 Jun 2020 23:46:27: 8000000 INFO @ Mon, 29 Jun 2020 23:46:30: 20000000 INFO @ Mon, 29 Jun 2020 23:46:32: 13000000 INFO @ Mon, 29 Jun 2020 23:46:34: 9000000 INFO @ Mon, 29 Jun 2020 23:46:37: 21000000 INFO @ Mon, 29 Jun 2020 23:46:39: 14000000 INFO @ Mon, 29 Jun 2020 23:46:41: 10000000 INFO @ Mon, 29 Jun 2020 23:46:43: 22000000 INFO @ Mon, 29 Jun 2020 23:46:46: 15000000 INFO @ Mon, 29 Jun 2020 23:46:48: 11000000 INFO @ Mon, 29 Jun 2020 23:46:49: 23000000 INFO @ Mon, 29 Jun 2020 23:46:52: 16000000 INFO @ Mon, 29 Jun 2020 23:46:54: 12000000 INFO @ Mon, 29 Jun 2020 23:46:55: 24000000 INFO @ Mon, 29 Jun 2020 23:46:59: 17000000 INFO @ Mon, 29 Jun 2020 23:47:01: 13000000 INFO @ Mon, 29 Jun 2020 23:47:02: 25000000 INFO @ Mon, 29 Jun 2020 23:47:06: 18000000 INFO @ Mon, 29 Jun 2020 23:47:08: 14000000 INFO @ Mon, 29 Jun 2020 23:47:08: 26000000 INFO @ Mon, 29 Jun 2020 23:47:13: 19000000 INFO @ Mon, 29 Jun 2020 23:47:14: 27000000 INFO @ Mon, 29 Jun 2020 23:47:15: 15000000 INFO @ Mon, 29 Jun 2020 23:47:15: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:47:15: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:47:15: #1 total tags in treatment: 27061334 INFO @ Mon, 29 Jun 2020 23:47:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:47:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:47:15: #1 tags after filtering in treatment: 27061334 INFO @ Mon, 29 Jun 2020 23:47:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:47:15: #1 finished! INFO @ Mon, 29 Jun 2020 23:47:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:47:17: #2 number of paired peaks: 332 WARNING @ Mon, 29 Jun 2020 23:47:17: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 29 Jun 2020 23:47:17: start model_add_line... INFO @ Mon, 29 Jun 2020 23:47:17: start X-correlation... INFO @ Mon, 29 Jun 2020 23:47:17: end of X-cor INFO @ Mon, 29 Jun 2020 23:47:17: #2 finished! INFO @ Mon, 29 Jun 2020 23:47:17: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:47:17: #2 alternative fragment length(s) may be 2,48,533,536,556,590 bps INFO @ Mon, 29 Jun 2020 23:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.05_model.r WARNING @ Mon, 29 Jun 2020 23:47:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:47:17: #2 You may need to consider one of the other alternative d(s): 2,48,533,536,556,590 WARNING @ Mon, 29 Jun 2020 23:47:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:47:17: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:47:20: 20000000 INFO @ Mon, 29 Jun 2020 23:47:21: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:47:27: 21000000 INFO @ Mon, 29 Jun 2020 23:47:28: 17000000 INFO @ Mon, 29 Jun 2020 23:47:34: 22000000 INFO @ Mon, 29 Jun 2020 23:47:35: 18000000 INFO @ Mon, 29 Jun 2020 23:47:41: 23000000 INFO @ Mon, 29 Jun 2020 23:47:41: 19000000 INFO @ Mon, 29 Jun 2020 23:47:48: 24000000 INFO @ Mon, 29 Jun 2020 23:47:48: 20000000 INFO @ Mon, 29 Jun 2020 23:47:55: 25000000 INFO @ Mon, 29 Jun 2020 23:47:55: 21000000 INFO @ Mon, 29 Jun 2020 23:48:01: 26000000 INFO @ Mon, 29 Jun 2020 23:48:02: 22000000 INFO @ Mon, 29 Jun 2020 23:48:02: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:48:08: 27000000 INFO @ Mon, 29 Jun 2020 23:48:09: 23000000 INFO @ Mon, 29 Jun 2020 23:48:09: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:48:09: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:48:09: #1 total tags in treatment: 27061334 INFO @ Mon, 29 Jun 2020 23:48:09: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:48:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:48:09: #1 tags after filtering in treatment: 27061334 INFO @ Mon, 29 Jun 2020 23:48:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:48:09: #1 finished! INFO @ Mon, 29 Jun 2020 23:48:09: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:48:11: #2 number of paired peaks: 332 WARNING @ Mon, 29 Jun 2020 23:48:11: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 29 Jun 2020 23:48:11: start model_add_line... INFO @ Mon, 29 Jun 2020 23:48:11: start X-correlation... INFO @ Mon, 29 Jun 2020 23:48:11: end of X-cor INFO @ Mon, 29 Jun 2020 23:48:11: #2 finished! INFO @ Mon, 29 Jun 2020 23:48:11: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:48:11: #2 alternative fragment length(s) may be 2,48,533,536,556,590 bps INFO @ Mon, 29 Jun 2020 23:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.10_model.r WARNING @ Mon, 29 Jun 2020 23:48:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:48:11: #2 You may need to consider one of the other alternative d(s): 2,48,533,536,556,590 WARNING @ Mon, 29 Jun 2020 23:48:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:48:11: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:48:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:48:15: 24000000 INFO @ Mon, 29 Jun 2020 23:48:21: 25000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.05_summits.bed INFO @ Mon, 29 Jun 2020 23:48:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4133 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:48:28: 26000000 INFO @ Mon, 29 Jun 2020 23:48:34: 27000000 INFO @ Mon, 29 Jun 2020 23:48:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:48:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:48:35: #1 total tags in treatment: 27061334 INFO @ Mon, 29 Jun 2020 23:48:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:48:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:48:35: #1 tags after filtering in treatment: 27061334 INFO @ Mon, 29 Jun 2020 23:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:48:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:48:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:48:37: #2 number of paired peaks: 332 WARNING @ Mon, 29 Jun 2020 23:48:37: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 29 Jun 2020 23:48:37: start model_add_line... INFO @ Mon, 29 Jun 2020 23:48:37: start X-correlation... INFO @ Mon, 29 Jun 2020 23:48:37: end of X-cor INFO @ Mon, 29 Jun 2020 23:48:37: #2 finished! INFO @ Mon, 29 Jun 2020 23:48:37: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:48:37: #2 alternative fragment length(s) may be 2,48,533,536,556,590 bps INFO @ Mon, 29 Jun 2020 23:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.20_model.r WARNING @ Mon, 29 Jun 2020 23:48:37: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:48:37: #2 You may need to consider one of the other alternative d(s): 2,48,533,536,556,590 WARNING @ Mon, 29 Jun 2020 23:48:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:48:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:48:59: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:49:22: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.10_summits.bed INFO @ Mon, 29 Jun 2020 23:49:23: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2835 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664657/SRX4664657.20_summits.bed INFO @ Mon, 29 Jun 2020 23:49:44: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 3 millis CompletedMACS2peakCalling