Job ID = 6454642 SRX = SRX2422643 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:14 prefetch.2.10.7: 1) Downloading 'SRR5110257'... 2020-06-21T09:22:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:27:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:27:23 prefetch.2.10.7: 'SRR5110257' is valid 2020-06-21T09:27:23 prefetch.2.10.7: 1) 'SRR5110257' was downloaded successfully Read 15102330 spots for SRR5110257/SRR5110257.sra Written 15102330 spots for SRR5110257/SRR5110257.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:05 15102330 reads; of these: 15102330 (100.00%) were unpaired; of these: 415137 (2.75%) aligned 0 times 10296191 (68.18%) aligned exactly 1 time 4391002 (29.07%) aligned >1 times 97.25% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 2162970 / 14687193 = 0.1473 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 18:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.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 18:37:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:32: 1000000 INFO @ Sun, 21 Jun 2020 18:37:38: 2000000 INFO @ Sun, 21 Jun 2020 18:37:44: 3000000 INFO @ Sun, 21 Jun 2020 18:37:50: 4000000 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 18:37:56: 5000000 INFO @ Sun, 21 Jun 2020 18:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.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 18:38:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:03: 6000000 INFO @ Sun, 21 Jun 2020 18:38:07: 1000000 INFO @ Sun, 21 Jun 2020 18:38:10: 7000000 INFO @ Sun, 21 Jun 2020 18:38:14: 2000000 INFO @ Sun, 21 Jun 2020 18:38:17: 8000000 INFO @ Sun, 21 Jun 2020 18:38:21: 3000000 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 18:38:24: 9000000 INFO @ Sun, 21 Jun 2020 18:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.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 18:38:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:28: 4000000 INFO @ Sun, 21 Jun 2020 18:38:31: 10000000 INFO @ Sun, 21 Jun 2020 18:38:33: 1000000 INFO @ Sun, 21 Jun 2020 18:38:35: 5000000 INFO @ Sun, 21 Jun 2020 18:38:38: 11000000 INFO @ Sun, 21 Jun 2020 18:38:40: 2000000 INFO @ Sun, 21 Jun 2020 18:38:43: 6000000 INFO @ Sun, 21 Jun 2020 18:38:46: 12000000 INFO @ Sun, 21 Jun 2020 18:38:47: 3000000 INFO @ Sun, 21 Jun 2020 18:38:49: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:38:49: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:38:49: #1 total tags in treatment: 12524223 INFO @ Sun, 21 Jun 2020 18:38:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:49: #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 18:38:50: 7000000 INFO @ Sun, 21 Jun 2020 18:38:50: #1 tags after filtering in treatment: 12524092 INFO @ Sun, 21 Jun 2020 18:38:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:51: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 18:38:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:51: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 18:38:51: #2 alternative fragment length(s) may be 3,90 bps INFO @ Sun, 21 Jun 2020 18:38:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.05_model.r WARNING @ Sun, 21 Jun 2020 18:38:51: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:51: #2 You may need to consider one of the other alternative d(s): 3,90 WARNING @ Sun, 21 Jun 2020 18:38:51: #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 18:38:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:54: 4000000 INFO @ Sun, 21 Jun 2020 18:38:57: 8000000 INFO @ Sun, 21 Jun 2020 18:39:01: 5000000 INFO @ Sun, 21 Jun 2020 18:39:04: 9000000 INFO @ Sun, 21 Jun 2020 18:39:08: 6000000 INFO @ Sun, 21 Jun 2020 18:39:11: 10000000 INFO @ Sun, 21 Jun 2020 18:39:15: 7000000 INFO @ Sun, 21 Jun 2020 18:39:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:19: 11000000 INFO @ Sun, 21 Jun 2020 18:39:22: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:26: 12000000 INFO @ Sun, 21 Jun 2020 18:39:30: 9000000 INFO @ Sun, 21 Jun 2020 18:39:30: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:39:30: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:39:30: #1 total tags in treatment: 12524223 INFO @ Sun, 21 Jun 2020 18:39:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:30: #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 18:39:30: #1 tags after filtering in treatment: 12524092 INFO @ Sun, 21 Jun 2020 18:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:30: Done! pass1 - making usageList (638 chroms): 1 millis pass2 - checking and writing primary data (3185 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:31: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 18:39:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:31: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 18:39:31: #2 alternative fragment length(s) may be 3,90 bps INFO @ Sun, 21 Jun 2020 18:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.10_model.r WARNING @ Sun, 21 Jun 2020 18:39:31: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:31: #2 You may need to consider one of the other alternative d(s): 3,90 WARNING @ Sun, 21 Jun 2020 18:39:31: #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 18:39:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:36: 10000000 INFO @ Sun, 21 Jun 2020 18:39:43: 11000000 INFO @ Sun, 21 Jun 2020 18:39:49: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:39:53: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:39:53: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:39:53: #1 total tags in treatment: 12524223 INFO @ Sun, 21 Jun 2020 18:39:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:53: #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 18:39:53: #1 tags after filtering in treatment: 12524092 INFO @ Sun, 21 Jun 2020 18:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:54: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 18:39:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:54: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 18:39:54: #2 alternative fragment length(s) may be 3,90 bps INFO @ Sun, 21 Jun 2020 18:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.20_model.r WARNING @ Sun, 21 Jun 2020 18:39:54: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:54: #2 You may need to consider one of the other alternative d(s): 3,90 WARNING @ Sun, 21 Jun 2020 18:39:54: #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 18:39:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:10: Done! pass1 - making usageList (470 chroms): 1 millis pass2 - checking and writing primary data (1678 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422643/SRX2422643.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:33: Done! pass1 - making usageList (251 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 18 millis CompletedMACS2peakCalling