Job ID = 6627098 SRX = SRX7780049 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:53 26808455 reads; of these: 26808455 (100.00%) were unpaired; of these: 3903364 (14.56%) aligned 0 times 16911435 (63.08%) aligned exactly 1 time 5993656 (22.36%) aligned >1 times 85.44% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 5913913 / 22905091 = 0.2582 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 @ Tue, 14 Jul 2020 10:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.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 @ Tue, 14 Jul 2020 10:04:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:04:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:04:17: 1000000 INFO @ Tue, 14 Jul 2020 10:04:23: 2000000 INFO @ Tue, 14 Jul 2020 10:04:30: 3000000 INFO @ Tue, 14 Jul 2020 10:04:36: 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 @ Tue, 14 Jul 2020 10:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.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 @ Tue, 14 Jul 2020 10:04:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:04:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:04:43: 5000000 INFO @ Tue, 14 Jul 2020 10:04:47: 1000000 INFO @ Tue, 14 Jul 2020 10:04:50: 6000000 INFO @ Tue, 14 Jul 2020 10:04:53: 2000000 INFO @ Tue, 14 Jul 2020 10:04:57: 7000000 INFO @ Tue, 14 Jul 2020 10:04:59: 3000000 INFO @ Tue, 14 Jul 2020 10:05:04: 8000000 INFO @ Tue, 14 Jul 2020 10:05:06: 4000000 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 @ Tue, 14 Jul 2020 10:05:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.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 @ Tue, 14 Jul 2020 10:05:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:05:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:05:11: 9000000 INFO @ Tue, 14 Jul 2020 10:05:12: 5000000 INFO @ Tue, 14 Jul 2020 10:05:17: 1000000 INFO @ Tue, 14 Jul 2020 10:05:18: 10000000 INFO @ Tue, 14 Jul 2020 10:05:18: 6000000 INFO @ Tue, 14 Jul 2020 10:05:23: 2000000 INFO @ Tue, 14 Jul 2020 10:05:25: 7000000 INFO @ Tue, 14 Jul 2020 10:05:25: 11000000 INFO @ Tue, 14 Jul 2020 10:05:30: 3000000 INFO @ Tue, 14 Jul 2020 10:05:31: 8000000 INFO @ Tue, 14 Jul 2020 10:05:32: 12000000 INFO @ Tue, 14 Jul 2020 10:05:36: 4000000 INFO @ Tue, 14 Jul 2020 10:05:38: 9000000 INFO @ Tue, 14 Jul 2020 10:05:39: 13000000 INFO @ Tue, 14 Jul 2020 10:05:42: 5000000 INFO @ Tue, 14 Jul 2020 10:05:44: 10000000 INFO @ Tue, 14 Jul 2020 10:05:46: 14000000 INFO @ Tue, 14 Jul 2020 10:05:49: 6000000 INFO @ Tue, 14 Jul 2020 10:05:50: 11000000 INFO @ Tue, 14 Jul 2020 10:05:53: 15000000 INFO @ Tue, 14 Jul 2020 10:05:55: 7000000 INFO @ Tue, 14 Jul 2020 10:05:57: 12000000 INFO @ Tue, 14 Jul 2020 10:06:00: 16000000 INFO @ Tue, 14 Jul 2020 10:06:02: 8000000 INFO @ Tue, 14 Jul 2020 10:06:03: 13000000 INFO @ Tue, 14 Jul 2020 10:06:07: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:06:07: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:06:07: #1 total tags in treatment: 16991178 INFO @ Tue, 14 Jul 2020 10:06:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:06:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:06:08: #1 tags after filtering in treatment: 16991115 INFO @ Tue, 14 Jul 2020 10:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:06:08: #1 finished! INFO @ Tue, 14 Jul 2020 10:06:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:06:08: 9000000 INFO @ Tue, 14 Jul 2020 10:06:09: #2 number of paired peaks: 144 WARNING @ Tue, 14 Jul 2020 10:06:09: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 14 Jul 2020 10:06:09: start model_add_line... INFO @ Tue, 14 Jul 2020 10:06:09: start X-correlation... INFO @ Tue, 14 Jul 2020 10:06:09: end of X-cor INFO @ Tue, 14 Jul 2020 10:06:09: #2 finished! INFO @ Tue, 14 Jul 2020 10:06:09: #2 predicted fragment length is 154 bps INFO @ Tue, 14 Jul 2020 10:06:09: #2 alternative fragment length(s) may be 55,82,110,140,154,207,261,522,563 bps INFO @ Tue, 14 Jul 2020 10:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.05_model.r INFO @ Tue, 14 Jul 2020 10:06:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:06:10: 14000000 INFO @ Tue, 14 Jul 2020 10:06:14: 10000000 INFO @ Tue, 14 Jul 2020 10:06:16: 15000000 INFO @ Tue, 14 Jul 2020 10:06:21: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:06:23: 16000000 INFO @ Tue, 14 Jul 2020 10:06:27: 12000000 INFO @ Tue, 14 Jul 2020 10:06:29: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:06:29: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:06:29: #1 total tags in treatment: 16991178 INFO @ Tue, 14 Jul 2020 10:06:29: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:06:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:06:30: #1 tags after filtering in treatment: 16991115 INFO @ Tue, 14 Jul 2020 10:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:06:30: #1 finished! INFO @ Tue, 14 Jul 2020 10:06:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:06:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:06:31: #2 number of paired peaks: 144 WARNING @ Tue, 14 Jul 2020 10:06:31: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 14 Jul 2020 10:06:31: start model_add_line... INFO @ Tue, 14 Jul 2020 10:06:31: start X-correlation... INFO @ Tue, 14 Jul 2020 10:06:31: end of X-cor INFO @ Tue, 14 Jul 2020 10:06:31: #2 finished! INFO @ Tue, 14 Jul 2020 10:06:31: #2 predicted fragment length is 154 bps INFO @ Tue, 14 Jul 2020 10:06:31: #2 alternative fragment length(s) may be 55,82,110,140,154,207,261,522,563 bps INFO @ Tue, 14 Jul 2020 10:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.10_model.r INFO @ Tue, 14 Jul 2020 10:06:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:06:33: 13000000 INFO @ Tue, 14 Jul 2020 10:06:39: 14000000 INFO @ Tue, 14 Jul 2020 10:06:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:06:45: 15000000 INFO @ Tue, 14 Jul 2020 10:06:51: 16000000 INFO @ Tue, 14 Jul 2020 10:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.05_summits.bed INFO @ Tue, 14 Jul 2020 10:06:56: Done! pass1 - making usageList (470 chroms): 1 millis INFO @ Tue, 14 Jul 2020 10:06:56: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:06:56: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:06:56: #1 total tags in treatment: 16991178 INFO @ Tue, 14 Jul 2020 10:06:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:06:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (1683 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:06:57: #1 tags after filtering in treatment: 16991115 INFO @ Tue, 14 Jul 2020 10:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:06:57: #1 finished! INFO @ Tue, 14 Jul 2020 10:06:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:06:57: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:06:58: #2 number of paired peaks: 144 WARNING @ Tue, 14 Jul 2020 10:06:58: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 14 Jul 2020 10:06:58: start model_add_line... INFO @ Tue, 14 Jul 2020 10:06:58: start X-correlation... INFO @ Tue, 14 Jul 2020 10:06:58: end of X-cor INFO @ Tue, 14 Jul 2020 10:06:58: #2 finished! INFO @ Tue, 14 Jul 2020 10:06:58: #2 predicted fragment length is 154 bps INFO @ Tue, 14 Jul 2020 10:06:58: #2 alternative fragment length(s) may be 55,82,110,140,154,207,261,522,563 bps INFO @ Tue, 14 Jul 2020 10:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.20_model.r INFO @ Tue, 14 Jul 2020 10:06:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:07:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.10_summits.bed INFO @ Tue, 14 Jul 2020 10:07:19: Done! pass1 - making usageList (372 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:07:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780049/SRX7780049.20_summits.bed INFO @ Tue, 14 Jul 2020 10:07:45: Done! pass1 - making usageList (111 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 5 millis CompletedMACS2peakCalling