Job ID = 6454414 SRX = SRX2055946 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:49 prefetch.2.10.7: 1) Downloading 'SRR4069178'... 2020-06-21T09:03:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:05:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:05:37 prefetch.2.10.7: 'SRR4069178' is valid 2020-06-21T09:05:37 prefetch.2.10.7: 1) 'SRR4069178' was downloaded successfully Read 17888908 spots for SRR4069178/SRR4069178.sra Written 17888908 spots for SRR4069178/SRR4069178.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: 00:06:28 17888908 reads; of these: 17888908 (100.00%) were unpaired; of these: 654105 (3.66%) aligned 0 times 10470242 (58.53%) aligned exactly 1 time 6764561 (37.81%) aligned >1 times 96.34% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 3241273 / 17234803 = 0.1881 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 18:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.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 18:16:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:59: 1000000 INFO @ Sun, 21 Jun 2020 18:17:04: 2000000 INFO @ Sun, 21 Jun 2020 18:17:09: 3000000 INFO @ Sun, 21 Jun 2020 18:17:14: 4000000 INFO @ Sun, 21 Jun 2020 18:17:18: 5000000 INFO @ Sun, 21 Jun 2020 18:17:23: 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 18:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.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 18:17:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:28: 7000000 INFO @ Sun, 21 Jun 2020 18:17:30: 1000000 INFO @ Sun, 21 Jun 2020 18:17:32: 8000000 INFO @ Sun, 21 Jun 2020 18:17:34: 2000000 INFO @ Sun, 21 Jun 2020 18:17:37: 9000000 INFO @ Sun, 21 Jun 2020 18:17:39: 3000000 INFO @ Sun, 21 Jun 2020 18:17:42: 10000000 INFO @ Sun, 21 Jun 2020 18:17:44: 4000000 INFO @ Sun, 21 Jun 2020 18:17:46: 11000000 INFO @ Sun, 21 Jun 2020 18:17:48: 5000000 INFO @ Sun, 21 Jun 2020 18:17:51: 12000000 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 18:17:53: 6000000 INFO @ Sun, 21 Jun 2020 18:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.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 18:17:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:56: 13000000 INFO @ Sun, 21 Jun 2020 18:17:58: 7000000 INFO @ Sun, 21 Jun 2020 18:18:00: 1000000 INFO @ Sun, 21 Jun 2020 18:18:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:18:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:18:01: #1 total tags in treatment: 13993530 INFO @ Sun, 21 Jun 2020 18:18:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:01: #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 18:18:02: #1 tags after filtering in treatment: 13993454 INFO @ Sun, 21 Jun 2020 18:18:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:03: 8000000 INFO @ Sun, 21 Jun 2020 18:18:03: #2 number of paired peaks: 2151 INFO @ Sun, 21 Jun 2020 18:18:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:03: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:18:03: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 18:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.05_model.r WARNING @ Sun, 21 Jun 2020 18:18:03: #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 18:18:03: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 18:18:03: #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 18:18:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:04: 2000000 INFO @ Sun, 21 Jun 2020 18:18:07: 9000000 INFO @ Sun, 21 Jun 2020 18:18:09: 3000000 INFO @ Sun, 21 Jun 2020 18:18:12: 10000000 INFO @ Sun, 21 Jun 2020 18:18:14: 4000000 INFO @ Sun, 21 Jun 2020 18:18:17: 11000000 INFO @ Sun, 21 Jun 2020 18:18:19: 5000000 INFO @ Sun, 21 Jun 2020 18:18:22: 12000000 INFO @ Sun, 21 Jun 2020 18:18:23: 6000000 INFO @ Sun, 21 Jun 2020 18:18:27: 13000000 INFO @ Sun, 21 Jun 2020 18:18:28: 7000000 INFO @ Sun, 21 Jun 2020 18:18:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:18:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:18:32: #1 total tags in treatment: 13993530 INFO @ Sun, 21 Jun 2020 18:18:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:32: #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 18:18:33: #1 tags after filtering in treatment: 13993454 INFO @ Sun, 21 Jun 2020 18:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:33: 8000000 INFO @ Sun, 21 Jun 2020 18:18:34: #2 number of paired peaks: 2151 INFO @ Sun, 21 Jun 2020 18:18:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:34: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:18:34: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 18:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.10_model.r WARNING @ Sun, 21 Jun 2020 18:18:34: #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 18:18:34: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 18:18:34: #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 18:18:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:38: 9000000 INFO @ Sun, 21 Jun 2020 18:18:43: 10000000 INFO @ Sun, 21 Jun 2020 18:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.05_summits.bed INFO @ Sun, 21 Jun 2020 18:18:44: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (2893 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:47: 11000000 INFO @ Sun, 21 Jun 2020 18:18:53: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:18:58: 13000000 INFO @ Sun, 21 Jun 2020 18:19:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:19:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:19:03: #1 total tags in treatment: 13993530 INFO @ Sun, 21 Jun 2020 18:19:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:03: #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 18:19:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:03: #1 tags after filtering in treatment: 13993454 INFO @ Sun, 21 Jun 2020 18:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:04: #2 number of paired peaks: 2151 INFO @ Sun, 21 Jun 2020 18:19:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:04: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:19:04: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 18:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.20_model.r WARNING @ Sun, 21 Jun 2020 18:19:04: #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 18:19:04: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 18:19:04: #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 18:19:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.10_summits.bed INFO @ Sun, 21 Jun 2020 18:19:18: Done! pass1 - making usageList (527 chroms): 2 millis pass2 - checking and writing primary data (2186 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:19:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055946/SRX2055946.20_summits.bed INFO @ Sun, 21 Jun 2020 18:19:50: Done! pass1 - making usageList (432 chroms): 1 millis pass2 - checking and writing primary data (1243 records, 4 fields): 15 millis CompletedMACS2peakCalling