Job ID = 6453634 SRX = SRX1308483 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:26:26 prefetch.2.10.7: 1) Downloading 'SRR2566781'... 2020-06-21T08:26:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:14 prefetch.2.10.7: 'SRR2566781' is valid 2020-06-21T08:28:14 prefetch.2.10.7: 1) 'SRR2566781' was downloaded successfully Read 8442753 spots for SRR2566781/SRR2566781.sra Written 8442753 spots for SRR2566781/SRR2566781.sra 2020-06-21T08:28:48 prefetch.2.10.7: 1) Downloading 'SRR2566782'... 2020-06-21T08:28:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:06 prefetch.2.10.7: 'SRR2566782' is valid 2020-06-21T08:31:06 prefetch.2.10.7: 1) 'SRR2566782' was downloaded successfully Read 8455419 spots for SRR2566782/SRR2566782.sra Written 8455419 spots for SRR2566782/SRR2566782.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: 00:04:27 16898172 reads; of these: 16898172 (100.00%) were unpaired; of these: 877293 (5.19%) aligned 0 times 12618951 (74.68%) aligned exactly 1 time 3401928 (20.13%) aligned >1 times 94.81% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 10508077 / 16020879 = 0.6559 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 17:39:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.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 17:39:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:35: 1000000 INFO @ Sun, 21 Jun 2020 17:39:42: 2000000 INFO @ Sun, 21 Jun 2020 17:39:48: 3000000 INFO @ Sun, 21 Jun 2020 17:39:54: 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 17:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.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 17:39:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:00: 5000000 INFO @ Sun, 21 Jun 2020 17:40:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:40:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:40:04: #1 total tags in treatment: 5512802 INFO @ Sun, 21 Jun 2020 17:40:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:04: #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 17:40:04: #1 tags after filtering in treatment: 5512787 INFO @ Sun, 21 Jun 2020 17:40:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:04: #2 number of paired peaks: 1231 INFO @ Sun, 21 Jun 2020 17:40:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:04: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:40:04: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 17:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.05_model.r WARNING @ Sun, 21 Jun 2020 17:40:04: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:40:04: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 17:40:04: #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 17:40:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:05: 1000000 INFO @ Sun, 21 Jun 2020 17:40:10: 2000000 INFO @ Sun, 21 Jun 2020 17:40:16: 3000000 INFO @ Sun, 21 Jun 2020 17:40:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:21: 4000000 INFO @ Sun, 21 Jun 2020 17:40:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.05_summits.bed INFO @ Sun, 21 Jun 2020 17:40:22: Done! pass1 - making usageList (542 chroms): 2 millis pass2 - checking and writing primary data (2156 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:26: 5000000 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 17:40:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:40:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:40:29: #1 total tags in treatment: 5512802 INFO @ Sun, 21 Jun 2020 17:40:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:29: #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 17:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.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 17:40:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:29: #1 tags after filtering in treatment: 5512787 INFO @ Sun, 21 Jun 2020 17:40:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:30: #2 number of paired peaks: 1231 INFO @ Sun, 21 Jun 2020 17:40:30: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:30: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:40:30: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 17:40:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.10_model.r WARNING @ Sun, 21 Jun 2020 17:40:30: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:40:30: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 17:40:30: #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 17:40:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:34: 1000000 INFO @ Sun, 21 Jun 2020 17:40:39: 2000000 INFO @ Sun, 21 Jun 2020 17:40:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:45: 3000000 INFO @ Sun, 21 Jun 2020 17:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.10_summits.bed INFO @ Sun, 21 Jun 2020 17:40:47: Done! pass1 - making usageList (478 chroms): 1 millis pass2 - checking and writing primary data (1781 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:40:55: 5000000 INFO @ Sun, 21 Jun 2020 17:40:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:40:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:40:58: #1 total tags in treatment: 5512802 INFO @ Sun, 21 Jun 2020 17:40:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:58: #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 17:40:59: #1 tags after filtering in treatment: 5512787 INFO @ Sun, 21 Jun 2020 17:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:59: #2 number of paired peaks: 1231 INFO @ Sun, 21 Jun 2020 17:40:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:59: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 17:40:59: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 17:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.20_model.r WARNING @ Sun, 21 Jun 2020 17:40:59: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:40:59: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 17:40:59: #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 17:40:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:41:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308483/SRX1308483.20_summits.bed INFO @ Sun, 21 Jun 2020 17:41:16: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (1006 records, 4 fields): 12 millis CompletedMACS2peakCalling