Job ID = 6457505 SRX = SRX4664659 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:44:18 prefetch.2.10.7: 1) Downloading 'SRR7813086'... 2020-06-21T11:44:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:46:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:46:45 prefetch.2.10.7: 'SRR7813086' is valid 2020-06-21T11:46:45 prefetch.2.10.7: 1) 'SRR7813086' was downloaded successfully Read 17456669 spots for SRR7813086/SRR7813086.sra Written 17456669 spots for SRR7813086/SRR7813086.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: 00:05:28 17456669 reads; of these: 17456669 (100.00%) were unpaired; of these: 509373 (2.92%) aligned 0 times 11836053 (67.80%) aligned exactly 1 time 5111243 (29.28%) aligned >1 times 97.08% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 2162700 / 16947296 = 0.1276 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 20:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.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 20:57:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:14: 1000000 INFO @ Sun, 21 Jun 2020 20:57:20: 2000000 INFO @ Sun, 21 Jun 2020 20:57:25: 3000000 INFO @ Sun, 21 Jun 2020 20:57:30: 4000000 INFO @ Sun, 21 Jun 2020 20:57:36: 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 20:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.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 20:57:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:41: 6000000 INFO @ Sun, 21 Jun 2020 20:57:45: 1000000 INFO @ Sun, 21 Jun 2020 20:57:47: 7000000 INFO @ Sun, 21 Jun 2020 20:57:50: 2000000 INFO @ Sun, 21 Jun 2020 20:57:52: 8000000 INFO @ Sun, 21 Jun 2020 20:57:55: 3000000 INFO @ Sun, 21 Jun 2020 20:57:58: 9000000 INFO @ Sun, 21 Jun 2020 20:58:01: 4000000 INFO @ Sun, 21 Jun 2020 20:58:03: 10000000 INFO @ Sun, 21 Jun 2020 20:58:06: 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 20:58:08: 11000000 INFO @ Sun, 21 Jun 2020 20:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.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 20:58:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:11: 6000000 INFO @ Sun, 21 Jun 2020 20:58:14: 12000000 INFO @ Sun, 21 Jun 2020 20:58:15: 1000000 INFO @ Sun, 21 Jun 2020 20:58:17: 7000000 INFO @ Sun, 21 Jun 2020 20:58:20: 13000000 INFO @ Sun, 21 Jun 2020 20:58:20: 2000000 INFO @ Sun, 21 Jun 2020 20:58:22: 8000000 INFO @ Sun, 21 Jun 2020 20:58:25: 14000000 INFO @ Sun, 21 Jun 2020 20:58:26: 3000000 INFO @ Sun, 21 Jun 2020 20:58:28: 9000000 INFO @ Sun, 21 Jun 2020 20:58:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:30: #1 total tags in treatment: 14784596 INFO @ Sun, 21 Jun 2020 20:58:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:30: #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 20:58:31: #1 tags after filtering in treatment: 14784514 INFO @ Sun, 21 Jun 2020 20:58:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:31: 4000000 INFO @ Sun, 21 Jun 2020 20:58:32: #2 number of paired peaks: 1224 INFO @ Sun, 21 Jun 2020 20:58:32: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:32: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:32: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:32: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:32: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:58:32: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 20:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.05_model.r WARNING @ Sun, 21 Jun 2020 20:58:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:32: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 20:58:32: #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 20:58:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:33: 10000000 INFO @ Sun, 21 Jun 2020 20:58:36: 5000000 INFO @ Sun, 21 Jun 2020 20:58:38: 11000000 INFO @ Sun, 21 Jun 2020 20:58:42: 6000000 INFO @ Sun, 21 Jun 2020 20:58:43: 12000000 INFO @ Sun, 21 Jun 2020 20:58:47: 7000000 INFO @ Sun, 21 Jun 2020 20:58:49: 13000000 INFO @ Sun, 21 Jun 2020 20:58:52: 8000000 INFO @ Sun, 21 Jun 2020 20:58:55: 14000000 INFO @ Sun, 21 Jun 2020 20:58:57: 9000000 INFO @ Sun, 21 Jun 2020 20:58:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:59: #1 total tags in treatment: 14784596 INFO @ Sun, 21 Jun 2020 20:58:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:59: #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 20:59:00: #1 tags after filtering in treatment: 14784514 INFO @ Sun, 21 Jun 2020 20:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:01: #2 number of paired peaks: 1224 INFO @ Sun, 21 Jun 2020 20:59:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:01: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:59:01: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 20:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.10_model.r WARNING @ Sun, 21 Jun 2020 20:59:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:59:01: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 20:59:01: #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 20:59:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:03: 10000000 INFO @ Sun, 21 Jun 2020 20:59:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:59:08: 11000000 INFO @ Sun, 21 Jun 2020 20:59:13: 12000000 INFO @ Sun, 21 Jun 2020 20:59:18: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.05_summits.bed INFO @ Sun, 21 Jun 2020 20:59:21: Done! pass1 - making usageList (541 chroms): 1 millis pass2 - checking and writing primary data (3060 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:59:23: 14000000 INFO @ Sun, 21 Jun 2020 20:59:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:59:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:59:28: #1 total tags in treatment: 14784596 INFO @ Sun, 21 Jun 2020 20:59:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:28: #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 20:59:28: #1 tags after filtering in treatment: 14784514 INFO @ Sun, 21 Jun 2020 20:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:29: #2 number of paired peaks: 1224 INFO @ Sun, 21 Jun 2020 20:59:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:29: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:59:29: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 20:59:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.20_model.r WARNING @ Sun, 21 Jun 2020 20:59:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:59:29: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 20:59:29: #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 20:59:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.10_summits.bed INFO @ Sun, 21 Jun 2020 20:59:49: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (1233 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:00:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664659/SRX4664659.20_summits.bed INFO @ Sun, 21 Jun 2020 21:00:18: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 19 millis CompletedMACS2peakCalling