Job ID = 6452690 SRX = SRX025490 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:42:21 prefetch.2.10.7: 1) Downloading 'SRR063896'... 2020-06-21T07:42:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:36 prefetch.2.10.7: 'SRR063896' is valid 2020-06-21T07:44:36 prefetch.2.10.7: 1) 'SRR063896' was downloaded successfully Read 23608065 spots for SRR063896/SRR063896.sra Written 23608065 spots for SRR063896/SRR063896.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: 00:08:32 23608065 reads; of these: 23608065 (100.00%) were unpaired; of these: 1333159 (5.65%) aligned 0 times 14105053 (59.75%) aligned exactly 1 time 8169853 (34.61%) aligned >1 times 94.35% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 15196467 / 22274906 = 0.6822 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 16:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.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 16:57:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:30: 1000000 INFO @ Sun, 21 Jun 2020 16:57:34: 2000000 INFO @ Sun, 21 Jun 2020 16:57:39: 3000000 INFO @ Sun, 21 Jun 2020 16:57:43: 4000000 INFO @ Sun, 21 Jun 2020 16:57:48: 5000000 INFO @ Sun, 21 Jun 2020 16:57:53: 6000000 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 16:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.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 16:57:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:57: 7000000 INFO @ Sun, 21 Jun 2020 16:57:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:58: #1 total tags in treatment: 7078439 INFO @ Sun, 21 Jun 2020 16:57:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:58: #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 16:57:58: #1 tags after filtering in treatment: 7078438 INFO @ Sun, 21 Jun 2020 16:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:58: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:59: #2 number of paired peaks: 1416 INFO @ Sun, 21 Jun 2020 16:57:59: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:59: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:59: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:59: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:59: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 16:57:59: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 16:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.05_model.r WARNING @ Sun, 21 Jun 2020 16:57:59: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:57:59: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 16:57:59: #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 16:57:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:00: 1000000 INFO @ Sun, 21 Jun 2020 16:58:04: 2000000 INFO @ Sun, 21 Jun 2020 16:58:09: 3000000 INFO @ Sun, 21 Jun 2020 16:58:13: 4000000 INFO @ Sun, 21 Jun 2020 16:58:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:18: 5000000 INFO @ Sun, 21 Jun 2020 16:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.05_summits.bed INFO @ Sun, 21 Jun 2020 16:58:21: Done! pass1 - making usageList (675 chroms): 1 millis pass2 - checking and writing primary data (3500 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:22: 6000000 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 16:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.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 16:58:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:27: 7000000 INFO @ Sun, 21 Jun 2020 16:58:27: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:27: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:27: #1 total tags in treatment: 7078439 INFO @ Sun, 21 Jun 2020 16:58:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:27: #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 16:58:28: #1 tags after filtering in treatment: 7078438 INFO @ Sun, 21 Jun 2020 16:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:28: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:28: #2 number of paired peaks: 1416 INFO @ Sun, 21 Jun 2020 16:58:28: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:28: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:28: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:28: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:28: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 16:58:28: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 16:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.10_model.r WARNING @ Sun, 21 Jun 2020 16:58:28: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:58:28: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 16:58:28: #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 16:58:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:30: 1000000 INFO @ Sun, 21 Jun 2020 16:58:34: 2000000 INFO @ Sun, 21 Jun 2020 16:58:38: 3000000 INFO @ Sun, 21 Jun 2020 16:58:43: 4000000 INFO @ Sun, 21 Jun 2020 16:58:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:47: 5000000 INFO @ Sun, 21 Jun 2020 16:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.10_summits.bed INFO @ Sun, 21 Jun 2020 16:58:51: Done! pass1 - making usageList (564 chroms): 1 millis pass2 - checking and writing primary data (2461 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:58:57: 7000000 INFO @ Sun, 21 Jun 2020 16:58:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:57: #1 total tags in treatment: 7078439 INFO @ Sun, 21 Jun 2020 16:58:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:57: #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 16:58:57: #1 tags after filtering in treatment: 7078438 INFO @ Sun, 21 Jun 2020 16:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:57: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:58: #2 number of paired peaks: 1416 INFO @ Sun, 21 Jun 2020 16:58:58: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:58: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 16:58:58: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 16:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.20_model.r WARNING @ Sun, 21 Jun 2020 16:58:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:58:58: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 16:58:58: #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 16:58:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:59:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025490/SRX025490.20_summits.bed INFO @ Sun, 21 Jun 2020 16:59:20: Done! pass1 - making usageList (385 chroms): 1 millis pass2 - checking and writing primary data (1043 records, 4 fields): 12 millis CompletedMACS2peakCalling