Job ID = 6453610 SRX = SRX1299936 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:37:09 prefetch.2.10.7: 1) Downloading 'SRR2546855'... 2020-06-21T08:37:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:58 prefetch.2.10.7: 1) 'SRR2546855' was downloaded successfully Read 20007312 spots for SRR2546855/SRR2546855.sra Written 20007312 spots for SRR2546855/SRR2546855.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: 00:04:50 20007312 reads; of these: 20007312 (100.00%) were unpaired; of these: 8166347 (40.82%) aligned 0 times 5747468 (28.73%) aligned exactly 1 time 6093497 (30.46%) aligned >1 times 59.18% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 5286249 / 11840965 = 0.4464 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 17:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.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 17:51:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:44: 1000000 INFO @ Sun, 21 Jun 2020 17:51:49: 2000000 INFO @ Sun, 21 Jun 2020 17:51:54: 3000000 INFO @ Sun, 21 Jun 2020 17:51:59: 4000000 INFO @ Sun, 21 Jun 2020 17:52:04: 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 17:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.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 17:52:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:10: 6000000 INFO @ Sun, 21 Jun 2020 17:52:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:52:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:52:13: #1 total tags in treatment: 6554716 INFO @ Sun, 21 Jun 2020 17:52:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:13: #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 17:52:13: #1 tags after filtering in treatment: 6554597 INFO @ Sun, 21 Jun 2020 17:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:13: #2 number of paired peaks: 1917 INFO @ Sun, 21 Jun 2020 17:52:13: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:14: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 17:52:14: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 17:52:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.05_model.r WARNING @ Sun, 21 Jun 2020 17:52:14: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:14: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 17:52:14: #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 17:52:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:14: 1000000 INFO @ Sun, 21 Jun 2020 17:52:19: 2000000 INFO @ Sun, 21 Jun 2020 17:52:24: 3000000 INFO @ Sun, 21 Jun 2020 17:52:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:29: 4000000 INFO @ Sun, 21 Jun 2020 17:52:35: 5000000 INFO @ Sun, 21 Jun 2020 17:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:35: Done! pass1 - making usageList (730 chroms): 1 millis pass2 - checking and writing primary data (3102 records, 4 fields): 21 millis CompletedMACS2peakCalling 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 17:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.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 17:52:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:39: 6000000 INFO @ Sun, 21 Jun 2020 17:52:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:52:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:52:43: #1 total tags in treatment: 6554716 INFO @ Sun, 21 Jun 2020 17:52:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:43: #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 17:52:43: #1 tags after filtering in treatment: 6554597 INFO @ Sun, 21 Jun 2020 17:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:44: #2 number of paired peaks: 1917 INFO @ Sun, 21 Jun 2020 17:52:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:44: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 17:52:44: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 17:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.10_model.r WARNING @ Sun, 21 Jun 2020 17:52:44: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:44: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 17:52:44: #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 17:52:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:45: 1000000 INFO @ Sun, 21 Jun 2020 17:52:50: 2000000 INFO @ Sun, 21 Jun 2020 17:52:55: 3000000 INFO @ Sun, 21 Jun 2020 17:52:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:00: 4000000 INFO @ Sun, 21 Jun 2020 17:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.10_summits.bed INFO @ Sun, 21 Jun 2020 17:53:04: Done! pass1 - making usageList (594 chroms): 1 millis pass2 - checking and writing primary data (1922 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:06: 5000000 INFO @ Sun, 21 Jun 2020 17:53:11: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:53:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:14: #1 total tags in treatment: 6554716 INFO @ Sun, 21 Jun 2020 17:53:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:14: #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 17:53:14: #1 tags after filtering in treatment: 6554597 INFO @ Sun, 21 Jun 2020 17:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:15: #2 number of paired peaks: 1917 INFO @ Sun, 21 Jun 2020 17:53:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:15: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 17:53:15: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sun, 21 Jun 2020 17:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:15: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:15: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sun, 21 Jun 2020 17:53:15: #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 17:53:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299936/SRX1299936.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:36: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (907 records, 4 fields): 12 millis CompletedMACS2peakCalling