Job ID = 6453671 SRX = SRX1361343 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:26 prefetch.2.10.7: 1) Downloading 'SRR2749781'... 2020-06-21T08:30:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:37:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:37:51 prefetch.2.10.7: 1) 'SRR2749781' was downloaded successfully Read 26035047 spots for SRR2749781/SRR2749781.sra Written 26035047 spots for SRR2749781/SRR2749781.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: 00:11:04 26035047 reads; of these: 26035047 (100.00%) were unpaired; of these: 847993 (3.26%) aligned 0 times 7343902 (28.21%) aligned exactly 1 time 17843152 (68.54%) aligned >1 times 96.74% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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 12 files... [bam_rmdupse_core] 11054239 / 25187054 = 0.4389 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 17:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.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 17:56:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:09: 1000000 INFO @ Sun, 21 Jun 2020 17:56:15: 2000000 INFO @ Sun, 21 Jun 2020 17:56:21: 3000000 INFO @ Sun, 21 Jun 2020 17:56:27: 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 17:56:33: 5000000 INFO @ Sun, 21 Jun 2020 17:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.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 17:56:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:39: 1000000 INFO @ Sun, 21 Jun 2020 17:56:39: 6000000 INFO @ Sun, 21 Jun 2020 17:56:45: 2000000 INFO @ Sun, 21 Jun 2020 17:56:45: 7000000 INFO @ Sun, 21 Jun 2020 17:56:51: 3000000 INFO @ Sun, 21 Jun 2020 17:56:51: 8000000 INFO @ Sun, 21 Jun 2020 17:56:57: 4000000 INFO @ Sun, 21 Jun 2020 17:56:57: 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 17:57:03: 5000000 INFO @ Sun, 21 Jun 2020 17:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.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 17:57:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:04: 10000000 INFO @ Sun, 21 Jun 2020 17:57:09: 6000000 INFO @ Sun, 21 Jun 2020 17:57:09: 1000000 INFO @ Sun, 21 Jun 2020 17:57:10: 11000000 INFO @ Sun, 21 Jun 2020 17:57:14: 2000000 INFO @ Sun, 21 Jun 2020 17:57:15: 7000000 INFO @ Sun, 21 Jun 2020 17:57:16: 12000000 INFO @ Sun, 21 Jun 2020 17:57:20: 3000000 INFO @ Sun, 21 Jun 2020 17:57:21: 8000000 INFO @ Sun, 21 Jun 2020 17:57:22: 13000000 INFO @ Sun, 21 Jun 2020 17:57:26: 4000000 INFO @ Sun, 21 Jun 2020 17:57:26: 9000000 INFO @ Sun, 21 Jun 2020 17:57:28: 14000000 INFO @ Sun, 21 Jun 2020 17:57:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:57:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:57:29: #1 total tags in treatment: 14132815 INFO @ Sun, 21 Jun 2020 17:57:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:29: #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 17:57:30: #1 tags after filtering in treatment: 14132767 INFO @ Sun, 21 Jun 2020 17:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:31: #2 number of paired peaks: 6214 INFO @ Sun, 21 Jun 2020 17:57:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:31: 5000000 INFO @ Sun, 21 Jun 2020 17:57:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:31: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 17:57:31: #2 alternative fragment length(s) may be 3,89 bps INFO @ Sun, 21 Jun 2020 17:57:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.05_model.r WARNING @ Sun, 21 Jun 2020 17:57:31: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:57:31: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Sun, 21 Jun 2020 17:57:31: #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 17:57:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:33: 10000000 INFO @ Sun, 21 Jun 2020 17:57:37: 6000000 INFO @ Sun, 21 Jun 2020 17:57:39: 11000000 INFO @ Sun, 21 Jun 2020 17:57:43: 7000000 INFO @ Sun, 21 Jun 2020 17:57:45: 12000000 INFO @ Sun, 21 Jun 2020 17:57:48: 8000000 INFO @ Sun, 21 Jun 2020 17:57:51: 13000000 INFO @ Sun, 21 Jun 2020 17:57:54: 9000000 INFO @ Sun, 21 Jun 2020 17:57:57: 14000000 INFO @ Sun, 21 Jun 2020 17:57:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:57:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:57:58: #1 total tags in treatment: 14132815 INFO @ Sun, 21 Jun 2020 17:57:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:58: #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 17:57:58: #1 tags after filtering in treatment: 14132767 INFO @ Sun, 21 Jun 2020 17:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:00: 10000000 INFO @ Sun, 21 Jun 2020 17:58:00: #2 number of paired peaks: 6214 INFO @ Sun, 21 Jun 2020 17:58:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:00: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 17:58:00: #2 alternative fragment length(s) may be 3,89 bps INFO @ Sun, 21 Jun 2020 17:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.10_model.r WARNING @ Sun, 21 Jun 2020 17:58:00: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:58:00: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Sun, 21 Jun 2020 17:58:00: #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 17:58:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:00: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:58:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:05: 11000000 INFO @ Sun, 21 Jun 2020 17:58:10: 12000000 INFO @ Sun, 21 Jun 2020 17:58:16: 13000000 INFO @ Sun, 21 Jun 2020 17:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.05_summits.bed INFO @ Sun, 21 Jun 2020 17:58:20: Done! INFO @ Sun, 21 Jun 2020 17:58:21: 14000000 pass1 - making usageList (1120 chroms): 4 millis pass2 - checking and writing primary data (8140 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:58:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:58:22: #1 total tags in treatment: 14132815 INFO @ Sun, 21 Jun 2020 17:58:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:22: #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 17:58:22: #1 tags after filtering in treatment: 14132767 INFO @ Sun, 21 Jun 2020 17:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:24: #2 number of paired peaks: 6214 INFO @ Sun, 21 Jun 2020 17:58:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:24: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 17:58:24: #2 alternative fragment length(s) may be 3,89 bps INFO @ Sun, 21 Jun 2020 17:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.20_model.r WARNING @ Sun, 21 Jun 2020 17:58:24: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:58:24: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Sun, 21 Jun 2020 17:58:24: #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 17:58:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:58:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.10_summits.bed INFO @ Sun, 21 Jun 2020 17:58:49: Done! pass1 - making usageList (993 chroms): 2 millis pass2 - checking and writing primary data (4124 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361343/SRX1361343.20_summits.bed INFO @ Sun, 21 Jun 2020 17:59:12: Done! pass1 - making usageList (815 chroms): 2 millis pass2 - checking and writing primary data (2298 records, 4 fields): 23 millis CompletedMACS2peakCalling