Job ID = 6457134 SRX = SRX447393 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:30:25 prefetch.2.10.7: 1) Downloading 'SRR1141009'... 2020-06-21T11:30:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:34:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:34:28 prefetch.2.10.7: 1) 'SRR1141009' was downloaded successfully Read 38691262 spots for SRR1141009/SRR1141009.sra Written 38691262 spots for SRR1141009/SRR1141009.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: 00:06:22 38691262 reads; of these: 38691262 (100.00%) were unpaired; of these: 8554208 (22.11%) aligned 0 times 24142004 (62.40%) aligned exactly 1 time 5995050 (15.49%) aligned >1 times 77.89% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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 8 files... [bam_rmdupse_core] 8249072 / 30137054 = 0.2737 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 20:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.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 20:48:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:48:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:48:48: 1000000 INFO @ Sun, 21 Jun 2020 20:48:53: 2000000 INFO @ Sun, 21 Jun 2020 20:48:58: 3000000 INFO @ Sun, 21 Jun 2020 20:49:02: 4000000 INFO @ Sun, 21 Jun 2020 20:49:07: 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 20:49:12: 6000000 INFO @ Sun, 21 Jun 2020 20:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.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 20:49:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:17: 7000000 INFO @ Sun, 21 Jun 2020 20:49:19: 1000000 INFO @ Sun, 21 Jun 2020 20:49:22: 8000000 INFO @ Sun, 21 Jun 2020 20:49:25: 2000000 INFO @ Sun, 21 Jun 2020 20:49:26: 9000000 INFO @ Sun, 21 Jun 2020 20:49:31: 3000000 INFO @ Sun, 21 Jun 2020 20:49:31: 10000000 INFO @ Sun, 21 Jun 2020 20:49:36: 11000000 INFO @ Sun, 21 Jun 2020 20:49:36: 4000000 INFO @ Sun, 21 Jun 2020 20:49:41: 12000000 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 20:49:42: 5000000 INFO @ Sun, 21 Jun 2020 20:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.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 20:49:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:46: 13000000 INFO @ Sun, 21 Jun 2020 20:49:48: 6000000 INFO @ Sun, 21 Jun 2020 20:49:48: 1000000 INFO @ Sun, 21 Jun 2020 20:49:51: 14000000 INFO @ Sun, 21 Jun 2020 20:49:53: 2000000 INFO @ Sun, 21 Jun 2020 20:49:53: 7000000 INFO @ Sun, 21 Jun 2020 20:49:56: 15000000 INFO @ Sun, 21 Jun 2020 20:49:58: 3000000 INFO @ Sun, 21 Jun 2020 20:49:59: 8000000 INFO @ Sun, 21 Jun 2020 20:50:01: 16000000 INFO @ Sun, 21 Jun 2020 20:50:03: 4000000 INFO @ Sun, 21 Jun 2020 20:50:05: 9000000 INFO @ Sun, 21 Jun 2020 20:50:05: 17000000 INFO @ Sun, 21 Jun 2020 20:50:08: 5000000 INFO @ Sun, 21 Jun 2020 20:50:10: 18000000 INFO @ Sun, 21 Jun 2020 20:50:10: 10000000 INFO @ Sun, 21 Jun 2020 20:50:13: 6000000 INFO @ Sun, 21 Jun 2020 20:50:16: 19000000 INFO @ Sun, 21 Jun 2020 20:50:16: 11000000 INFO @ Sun, 21 Jun 2020 20:50:18: 7000000 INFO @ Sun, 21 Jun 2020 20:50:21: 20000000 INFO @ Sun, 21 Jun 2020 20:50:21: 12000000 INFO @ Sun, 21 Jun 2020 20:50:23: 8000000 INFO @ Sun, 21 Jun 2020 20:50:26: 21000000 INFO @ Sun, 21 Jun 2020 20:50:27: 13000000 INFO @ Sun, 21 Jun 2020 20:50:28: 9000000 INFO @ Sun, 21 Jun 2020 20:50:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:50:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:50:30: #1 total tags in treatment: 21887982 INFO @ Sun, 21 Jun 2020 20:50:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:30: #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 20:50:31: #1 tags after filtering in treatment: 21887893 INFO @ Sun, 21 Jun 2020 20:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:32: 14000000 INFO @ Sun, 21 Jun 2020 20:50:32: #2 number of paired peaks: 538 WARNING @ Sun, 21 Jun 2020 20:50:32: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 21 Jun 2020 20:50:32: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:33: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:50:33: #2 alternative fragment length(s) may be 4,50,557 bps INFO @ Sun, 21 Jun 2020 20:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.05_model.r WARNING @ Sun, 21 Jun 2020 20:50:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:50:33: #2 You may need to consider one of the other alternative d(s): 4,50,557 WARNING @ Sun, 21 Jun 2020 20:50:33: #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 20:50:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:50:33: 10000000 INFO @ Sun, 21 Jun 2020 20:50:38: 11000000 INFO @ Sun, 21 Jun 2020 20:50:38: 15000000 INFO @ Sun, 21 Jun 2020 20:50:43: 12000000 INFO @ Sun, 21 Jun 2020 20:50:43: 16000000 INFO @ Sun, 21 Jun 2020 20:50:48: 13000000 INFO @ Sun, 21 Jun 2020 20:50:49: 17000000 INFO @ Sun, 21 Jun 2020 20:50:52: 14000000 INFO @ Sun, 21 Jun 2020 20:50:54: 18000000 INFO @ Sun, 21 Jun 2020 20:50:57: 15000000 INFO @ Sun, 21 Jun 2020 20:51:00: 19000000 INFO @ Sun, 21 Jun 2020 20:51:02: 16000000 INFO @ Sun, 21 Jun 2020 20:51:06: 20000000 INFO @ Sun, 21 Jun 2020 20:51:07: 17000000 INFO @ Sun, 21 Jun 2020 20:51:11: 21000000 INFO @ Sun, 21 Jun 2020 20:51:12: 18000000 INFO @ Sun, 21 Jun 2020 20:51:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:51:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:51:17: #1 total tags in treatment: 21887982 INFO @ Sun, 21 Jun 2020 20:51:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:17: #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 20:51:17: #1 tags after filtering in treatment: 21887893 INFO @ Sun, 21 Jun 2020 20:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:18: 19000000 INFO @ Sun, 21 Jun 2020 20:51:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:19: #2 number of paired peaks: 538 WARNING @ Sun, 21 Jun 2020 20:51:19: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 21 Jun 2020 20:51:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:19: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:51:19: #2 alternative fragment length(s) may be 4,50,557 bps INFO @ Sun, 21 Jun 2020 20:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.10_model.r WARNING @ Sun, 21 Jun 2020 20:51:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:19: #2 You may need to consider one of the other alternative d(s): 4,50,557 WARNING @ Sun, 21 Jun 2020 20:51:19: #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 20:51:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:23: 20000000 INFO @ Sun, 21 Jun 2020 20:51:27: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:51:32: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:51:32: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:51:32: #1 total tags in treatment: 21887982 INFO @ Sun, 21 Jun 2020 20:51:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:32: #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 20:51:33: #1 tags after filtering in treatment: 21887893 INFO @ Sun, 21 Jun 2020 20:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:34: #2 number of paired peaks: 538 WARNING @ Sun, 21 Jun 2020 20:51:34: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 21 Jun 2020 20:51:34: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:34: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:34: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:34: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:34: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:51:34: #2 alternative fragment length(s) may be 4,50,557 bps INFO @ Sun, 21 Jun 2020 20:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.20_model.r WARNING @ Sun, 21 Jun 2020 20:51:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:34: #2 You may need to consider one of the other alternative d(s): 4,50,557 WARNING @ Sun, 21 Jun 2020 20:51:34: #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 20:51:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.05_summits.bed INFO @ Sun, 21 Jun 2020 20:51:41: Done! pass1 - making usageList (404 chroms): 2 millis pass2 - checking and writing primary data (9567 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:52:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.10_summits.bed INFO @ Sun, 21 Jun 2020 20:52:28: Done! pass1 - making usageList (292 chroms): 1 millis pass2 - checking and writing primary data (4444 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX447393/SRX447393.20_summits.bed INFO @ Sun, 21 Jun 2020 20:52:38: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (1741 records, 4 fields): 7 millis CompletedMACS2peakCalling