Job ID = 6529220 SRX = SRX1032405 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: 00:08:08 27744920 reads; of these: 27744920 (100.00%) were unpaired; of these: 709124 (2.56%) aligned 0 times 20264330 (73.04%) aligned exactly 1 time 6771466 (24.41%) aligned >1 times 97.44% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 3511398 / 27035796 = 0.1299 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, 30 Jun 2020 01:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.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, 30 Jun 2020 01:57:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:45: 1000000 INFO @ Tue, 30 Jun 2020 01:57:52: 2000000 INFO @ Tue, 30 Jun 2020 01:57:58: 3000000 INFO @ Tue, 30 Jun 2020 01:58:04: 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, 30 Jun 2020 01:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.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, 30 Jun 2020 01:58:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:10: 5000000 INFO @ Tue, 30 Jun 2020 01:58:16: 6000000 INFO @ Tue, 30 Jun 2020 01:58:16: 1000000 INFO @ Tue, 30 Jun 2020 01:58:22: 7000000 INFO @ Tue, 30 Jun 2020 01:58:23: 2000000 INFO @ Tue, 30 Jun 2020 01:58:28: 8000000 INFO @ Tue, 30 Jun 2020 01:58:30: 3000000 INFO @ Tue, 30 Jun 2020 01:58:35: 9000000 INFO @ Tue, 30 Jun 2020 01:58:37: 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, 30 Jun 2020 01:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.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, 30 Jun 2020 01:58:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:41: 10000000 INFO @ Tue, 30 Jun 2020 01:58:44: 5000000 INFO @ Tue, 30 Jun 2020 01:58:46: 1000000 INFO @ Tue, 30 Jun 2020 01:58:48: 11000000 INFO @ Tue, 30 Jun 2020 01:58:51: 6000000 INFO @ Tue, 30 Jun 2020 01:58:52: 2000000 INFO @ Tue, 30 Jun 2020 01:58:54: 12000000 INFO @ Tue, 30 Jun 2020 01:58:58: 7000000 INFO @ Tue, 30 Jun 2020 01:58:59: 3000000 INFO @ Tue, 30 Jun 2020 01:59:01: 13000000 INFO @ Tue, 30 Jun 2020 01:59:05: 8000000 INFO @ Tue, 30 Jun 2020 01:59:05: 4000000 INFO @ Tue, 30 Jun 2020 01:59:07: 14000000 INFO @ Tue, 30 Jun 2020 01:59:11: 5000000 INFO @ Tue, 30 Jun 2020 01:59:12: 9000000 INFO @ Tue, 30 Jun 2020 01:59:13: 15000000 INFO @ Tue, 30 Jun 2020 01:59:18: 6000000 INFO @ Tue, 30 Jun 2020 01:59:19: 10000000 INFO @ Tue, 30 Jun 2020 01:59:19: 16000000 INFO @ Tue, 30 Jun 2020 01:59:24: 7000000 INFO @ Tue, 30 Jun 2020 01:59:26: 17000000 INFO @ Tue, 30 Jun 2020 01:59:26: 11000000 INFO @ Tue, 30 Jun 2020 01:59:30: 8000000 INFO @ Tue, 30 Jun 2020 01:59:32: 18000000 INFO @ Tue, 30 Jun 2020 01:59:33: 12000000 INFO @ Tue, 30 Jun 2020 01:59:37: 9000000 INFO @ Tue, 30 Jun 2020 01:59:39: 19000000 INFO @ Tue, 30 Jun 2020 01:59:40: 13000000 INFO @ Tue, 30 Jun 2020 01:59:43: 10000000 INFO @ Tue, 30 Jun 2020 01:59:45: 20000000 INFO @ Tue, 30 Jun 2020 01:59:47: 14000000 INFO @ Tue, 30 Jun 2020 01:59:50: 11000000 INFO @ Tue, 30 Jun 2020 01:59:52: 21000000 INFO @ Tue, 30 Jun 2020 01:59:53: 15000000 INFO @ Tue, 30 Jun 2020 01:59:56: 12000000 INFO @ Tue, 30 Jun 2020 01:59:58: 22000000 INFO @ Tue, 30 Jun 2020 02:00:00: 16000000 INFO @ Tue, 30 Jun 2020 02:00:03: 13000000 INFO @ Tue, 30 Jun 2020 02:00:04: 23000000 INFO @ Tue, 30 Jun 2020 02:00:07: 17000000 INFO @ Tue, 30 Jun 2020 02:00:08: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:00:08: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:00:08: #1 total tags in treatment: 23524398 INFO @ Tue, 30 Jun 2020 02:00:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:00:08: #1 tags after filtering in treatment: 23524396 INFO @ Tue, 30 Jun 2020 02:00:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:09: 14000000 INFO @ Tue, 30 Jun 2020 02:00:10: #2 number of paired peaks: 342 WARNING @ Tue, 30 Jun 2020 02:00:10: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:10: #2 predicted fragment length is 105 bps INFO @ Tue, 30 Jun 2020 02:00:10: #2 alternative fragment length(s) may be 4,105 bps INFO @ Tue, 30 Jun 2020 02:00:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.05_model.r INFO @ Tue, 30 Jun 2020 02:00:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:00:14: 18000000 INFO @ Tue, 30 Jun 2020 02:00:15: 15000000 INFO @ Tue, 30 Jun 2020 02:00:21: 19000000 INFO @ Tue, 30 Jun 2020 02:00:21: 16000000 INFO @ Tue, 30 Jun 2020 02:00:27: 17000000 INFO @ Tue, 30 Jun 2020 02:00:27: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:00:33: 18000000 INFO @ Tue, 30 Jun 2020 02:00:34: 21000000 INFO @ Tue, 30 Jun 2020 02:00:40: 19000000 INFO @ Tue, 30 Jun 2020 02:00:40: 22000000 INFO @ Tue, 30 Jun 2020 02:00:46: 20000000 INFO @ Tue, 30 Jun 2020 02:00:47: 23000000 INFO @ Tue, 30 Jun 2020 02:00:51: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:00:51: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:00:51: #1 total tags in treatment: 23524398 INFO @ Tue, 30 Jun 2020 02:00:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:00:52: #1 tags after filtering in treatment: 23524396 INFO @ Tue, 30 Jun 2020 02:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:52: 21000000 INFO @ Tue, 30 Jun 2020 02:00:53: #2 number of paired peaks: 342 WARNING @ Tue, 30 Jun 2020 02:00:53: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:53: #2 predicted fragment length is 105 bps INFO @ Tue, 30 Jun 2020 02:00:53: #2 alternative fragment length(s) may be 4,105 bps INFO @ Tue, 30 Jun 2020 02:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.10_model.r INFO @ Tue, 30 Jun 2020 02:00:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:00:58: 22000000 INFO @ Tue, 30 Jun 2020 02:01:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:01:04: 23000000 INFO @ Tue, 30 Jun 2020 02:01:07: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:01:07: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:01:07: #1 total tags in treatment: 23524398 INFO @ Tue, 30 Jun 2020 02:01:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:01:08: #1 tags after filtering in treatment: 23524396 INFO @ Tue, 30 Jun 2020 02:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:10: #2 number of paired peaks: 342 WARNING @ Tue, 30 Jun 2020 02:01:10: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:10: #2 predicted fragment length is 105 bps INFO @ Tue, 30 Jun 2020 02:01:10: #2 alternative fragment length(s) may be 4,105 bps INFO @ Tue, 30 Jun 2020 02:01:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.20_model.r INFO @ Tue, 30 Jun 2020 02:01:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.05_summits.bed INFO @ Tue, 30 Jun 2020 02:01:26: Done! pass1 - making usageList (764 chroms): 2 millis pass2 - checking and writing primary data (7235 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:01:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.10_summits.bed INFO @ Tue, 30 Jun 2020 02:02:09: Done! pass1 - making usageList (653 chroms): 2 millis pass2 - checking and writing primary data (2523 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032405/SRX1032405.20_summits.bed INFO @ Tue, 30 Jun 2020 02:02:27: Done! pass1 - making usageList (499 chroms): 1 millis pass2 - checking and writing primary data (1158 records, 4 fields): 16 millis CompletedMACS2peakCalling