Job ID = 6454185 SRX = SRX1850482 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:24 prefetch.2.10.7: 1) Downloading 'SRR3675039'... 2020-06-21T09:13:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:19:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:19:26 prefetch.2.10.7: 1) 'SRR3675039' was downloaded successfully Read 16543983 spots for SRR3675039/SRR3675039.sra Written 16543983 spots for SRR3675039/SRR3675039.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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:12 16543983 reads; of these: 16543983 (100.00%) were unpaired; of these: 695296 (4.20%) aligned 0 times 13360004 (80.75%) aligned exactly 1 time 2488683 (15.04%) aligned >1 times 95.80% overall alignment rate Time searching: 00:08:15 Overall time: 00:08:15 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] 9525741 / 15848687 = 0.6010 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 18:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.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 18:33:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:18: 1000000 INFO @ Sun, 21 Jun 2020 18:33:26: 2000000 INFO @ Sun, 21 Jun 2020 18:33:34: 3000000 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 18:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.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 18:33:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:41: 4000000 INFO @ Sun, 21 Jun 2020 18:33:49: 1000000 INFO @ Sun, 21 Jun 2020 18:33:50: 5000000 INFO @ Sun, 21 Jun 2020 18:33:58: 2000000 INFO @ Sun, 21 Jun 2020 18:34:00: 6000000 INFO @ Sun, 21 Jun 2020 18:34:03: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:34:03: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:34:03: #1 total tags in treatment: 6322946 INFO @ Sun, 21 Jun 2020 18:34:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:03: #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 18:34:03: #1 tags after filtering in treatment: 6322705 INFO @ Sun, 21 Jun 2020 18:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:03: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 18:34:03: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 18:34:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:04: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 18:34:04: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 18:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.05_model.r WARNING @ Sun, 21 Jun 2020 18:34:04: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:04: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 18:34:04: #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 18:34:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:06: 3000000 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 18:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.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 18:34:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:14: 4000000 INFO @ Sun, 21 Jun 2020 18:34:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:19: 1000000 INFO @ Sun, 21 Jun 2020 18:34:23: 5000000 INFO @ Sun, 21 Jun 2020 18:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.05_summits.bed INFO @ Sun, 21 Jun 2020 18:34:24: Done! pass1 - making usageList (414 chroms): 1 millis pass2 - checking and writing primary data (1497 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:29: 2000000 INFO @ Sun, 21 Jun 2020 18:34:32: 6000000 INFO @ Sun, 21 Jun 2020 18:34:35: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:34:35: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:34:35: #1 total tags in treatment: 6322946 INFO @ Sun, 21 Jun 2020 18:34:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:35: #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 18:34:35: #1 tags after filtering in treatment: 6322705 INFO @ Sun, 21 Jun 2020 18:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:36: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 18:34:36: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 18:34:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:36: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 18:34:36: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 18:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.10_model.r WARNING @ Sun, 21 Jun 2020 18:34:36: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:36: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 18:34:36: #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 18:34:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:37: 3000000 INFO @ Sun, 21 Jun 2020 18:34:45: 4000000 INFO @ Sun, 21 Jun 2020 18:34:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:34:53: 5000000 INFO @ Sun, 21 Jun 2020 18:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:57: Done! pass1 - making usageList (264 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:02: 6000000 INFO @ Sun, 21 Jun 2020 18:35:04: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:35:04: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:35:04: #1 total tags in treatment: 6322946 INFO @ Sun, 21 Jun 2020 18:35:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:04: #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 18:35:05: #1 tags after filtering in treatment: 6322705 INFO @ Sun, 21 Jun 2020 18:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:05: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 18:35:05: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 18:35:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:05: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 18:35:05: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 18:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.20_model.r WARNING @ Sun, 21 Jun 2020 18:35:05: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:05: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 18:35:05: #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 18:35:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:35:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1850482/SRX1850482.20_summits.bed INFO @ Sun, 21 Jun 2020 18:35:26: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 4 millis CompletedMACS2peakCalling