Job ID = 6454626 SRX = SRX2422630 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:55 prefetch.2.10.7: 1) Downloading 'SRR5110244'... 2020-06-21T09:37:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:57 prefetch.2.10.7: 'SRR5110244' is valid 2020-06-21T09:39:57 prefetch.2.10.7: 1) 'SRR5110244' was downloaded successfully Read 13268284 spots for SRR5110244/SRR5110244.sra Written 13268284 spots for SRR5110244/SRR5110244.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: 00:04:38 13268284 reads; of these: 13268284 (100.00%) were unpaired; of these: 345463 (2.60%) aligned 0 times 8745523 (65.91%) aligned exactly 1 time 4177298 (31.48%) aligned >1 times 97.40% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 1582961 / 12922821 = 0.1225 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 18:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.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 18:49:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:13: 1000000 INFO @ Sun, 21 Jun 2020 18:49:19: 2000000 INFO @ Sun, 21 Jun 2020 18:49:25: 3000000 INFO @ Sun, 21 Jun 2020 18:49:31: 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 18:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.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 18:49:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:37: 5000000 INFO @ Sun, 21 Jun 2020 18:49:43: 1000000 INFO @ Sun, 21 Jun 2020 18:49:44: 6000000 INFO @ Sun, 21 Jun 2020 18:49:50: 2000000 INFO @ Sun, 21 Jun 2020 18:49:50: 7000000 INFO @ Sun, 21 Jun 2020 18:49:57: 3000000 INFO @ Sun, 21 Jun 2020 18:49:57: 8000000 INFO @ Sun, 21 Jun 2020 18:50:03: 4000000 INFO @ Sun, 21 Jun 2020 18:50:04: 9000000 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 18:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.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 18:50:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:11: 5000000 INFO @ Sun, 21 Jun 2020 18:50:11: 10000000 INFO @ Sun, 21 Jun 2020 18:50:15: 1000000 INFO @ Sun, 21 Jun 2020 18:50:19: 6000000 INFO @ Sun, 21 Jun 2020 18:50:19: 11000000 INFO @ Sun, 21 Jun 2020 18:50:22: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:50:22: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:50:22: #1 total tags in treatment: 11339860 INFO @ Sun, 21 Jun 2020 18:50:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:22: #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 18:50:22: #1 tags after filtering in treatment: 11339742 INFO @ Sun, 21 Jun 2020 18:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:23: 2000000 INFO @ Sun, 21 Jun 2020 18:50:23: #2 number of paired peaks: 1740 INFO @ Sun, 21 Jun 2020 18:50:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:23: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:50:23: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 18:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.05_model.r WARNING @ Sun, 21 Jun 2020 18:50:23: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:23: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 18:50:23: #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 18:50:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:26: 7000000 INFO @ Sun, 21 Jun 2020 18:50:31: 3000000 INFO @ Sun, 21 Jun 2020 18:50:33: 8000000 INFO @ Sun, 21 Jun 2020 18:50:39: 4000000 INFO @ Sun, 21 Jun 2020 18:50:40: 9000000 INFO @ Sun, 21 Jun 2020 18:50:47: 5000000 INFO @ Sun, 21 Jun 2020 18:50:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:48: 10000000 INFO @ Sun, 21 Jun 2020 18:50:55: 6000000 INFO @ Sun, 21 Jun 2020 18:50:55: 11000000 INFO @ Sun, 21 Jun 2020 18:50:58: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:50:58: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:50:58: #1 total tags in treatment: 11339860 INFO @ Sun, 21 Jun 2020 18:50:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:58: #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 18:50:58: #1 tags after filtering in treatment: 11339742 INFO @ Sun, 21 Jun 2020 18:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:59: Done! pass1 - making usageList (572 chroms): 1 millis pass2 - checking and writing primary data (2705 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:59: #2 number of paired peaks: 1740 INFO @ Sun, 21 Jun 2020 18:50:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:59: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:50:59: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 18:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.10_model.r WARNING @ Sun, 21 Jun 2020 18:50:59: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:59: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 18:50:59: #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 18:50:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:02: 7000000 INFO @ Sun, 21 Jun 2020 18:51:10: 8000000 INFO @ Sun, 21 Jun 2020 18:51:18: 9000000 INFO @ Sun, 21 Jun 2020 18:51:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:25: 10000000 INFO @ Sun, 21 Jun 2020 18:51:33: 11000000 INFO @ Sun, 21 Jun 2020 18:51:35: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:51:35: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:51:35: #1 total tags in treatment: 11339860 INFO @ Sun, 21 Jun 2020 18:51:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:35: #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 18:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:35: Done! INFO @ Sun, 21 Jun 2020 18:51:35: #1 tags after filtering in treatment: 11339742 INFO @ Sun, 21 Jun 2020 18:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:35: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:36: #2 number of paired peaks: 1740 INFO @ Sun, 21 Jun 2020 18:51:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:36: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:51:36: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 18:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.20_model.r WARNING @ Sun, 21 Jun 2020 18:51:37: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:37: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 18:51:37: #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 18:51:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422630/SRX2422630.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:12: Done! pass1 - making usageList (275 chroms): 0 millis pass2 - checking and writing primary data (614 records, 4 fields): 9 millis CompletedMACS2peakCalling