Job ID = 16439843 SRX = SRX8369900 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: 00:12:05 41614045 reads; of these: 41614045 (100.00%) were unpaired; of these: 5025430 (12.08%) aligned 0 times 29036694 (69.78%) aligned exactly 1 time 7551921 (18.15%) aligned >1 times 87.92% overall alignment rate Time searching: 00:12:05 Overall time: 00:12:05 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 16 files... [bam_rmdupse_core] 10963228 / 36588615 = 0.2996 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.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, 02 Aug 2022 16:39:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:39:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:39:53: 1000000 INFO @ Tue, 02 Aug 2022 16:39:59: 2000000 INFO @ Tue, 02 Aug 2022 16:40:04: 3000000 INFO @ Tue, 02 Aug 2022 16:40:10: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:40:15: 5000000 INFO @ Tue, 02 Aug 2022 16:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.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, 02 Aug 2022 16:40:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:40:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:40:21: 6000000 INFO @ Tue, 02 Aug 2022 16:40:22: 1000000 INFO @ Tue, 02 Aug 2022 16:40:27: 7000000 INFO @ Tue, 02 Aug 2022 16:40:28: 2000000 INFO @ Tue, 02 Aug 2022 16:40:34: 8000000 INFO @ Tue, 02 Aug 2022 16:40:35: 3000000 INFO @ Tue, 02 Aug 2022 16:40:40: 9000000 INFO @ Tue, 02 Aug 2022 16:40:41: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:40:46: 10000000 INFO @ Tue, 02 Aug 2022 16:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.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, 02 Aug 2022 16:40:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:40:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:40:47: 5000000 INFO @ Tue, 02 Aug 2022 16:40:52: 11000000 INFO @ Tue, 02 Aug 2022 16:40:53: 6000000 INFO @ Tue, 02 Aug 2022 16:40:54: 1000000 INFO @ Tue, 02 Aug 2022 16:40:59: 12000000 INFO @ Tue, 02 Aug 2022 16:41:00: 7000000 INFO @ Tue, 02 Aug 2022 16:41:02: 2000000 INFO @ Tue, 02 Aug 2022 16:41:05: 13000000 INFO @ Tue, 02 Aug 2022 16:41:06: 8000000 INFO @ Tue, 02 Aug 2022 16:41:09: 3000000 INFO @ Tue, 02 Aug 2022 16:41:11: 14000000 INFO @ Tue, 02 Aug 2022 16:41:13: 9000000 INFO @ Tue, 02 Aug 2022 16:41:17: 4000000 INFO @ Tue, 02 Aug 2022 16:41:18: 15000000 INFO @ Tue, 02 Aug 2022 16:41:19: 10000000 INFO @ Tue, 02 Aug 2022 16:41:24: 16000000 INFO @ Tue, 02 Aug 2022 16:41:25: 5000000 INFO @ Tue, 02 Aug 2022 16:41:25: 11000000 INFO @ Tue, 02 Aug 2022 16:41:30: 17000000 INFO @ Tue, 02 Aug 2022 16:41:32: 12000000 INFO @ Tue, 02 Aug 2022 16:41:33: 6000000 INFO @ Tue, 02 Aug 2022 16:41:36: 18000000 INFO @ Tue, 02 Aug 2022 16:41:38: 13000000 INFO @ Tue, 02 Aug 2022 16:41:40: 7000000 INFO @ Tue, 02 Aug 2022 16:41:43: 19000000 INFO @ Tue, 02 Aug 2022 16:41:44: 14000000 INFO @ Tue, 02 Aug 2022 16:41:48: 8000000 INFO @ Tue, 02 Aug 2022 16:41:49: 20000000 INFO @ Tue, 02 Aug 2022 16:41:51: 15000000 INFO @ Tue, 02 Aug 2022 16:41:56: 9000000 INFO @ Tue, 02 Aug 2022 16:41:57: 21000000 INFO @ Tue, 02 Aug 2022 16:41:57: 16000000 INFO @ Tue, 02 Aug 2022 16:42:03: 22000000 INFO @ Tue, 02 Aug 2022 16:42:03: 17000000 INFO @ Tue, 02 Aug 2022 16:42:04: 10000000 INFO @ Tue, 02 Aug 2022 16:42:10: 23000000 INFO @ Tue, 02 Aug 2022 16:42:10: 18000000 INFO @ Tue, 02 Aug 2022 16:42:12: 11000000 INFO @ Tue, 02 Aug 2022 16:42:16: 24000000 INFO @ Tue, 02 Aug 2022 16:42:16: 19000000 INFO @ Tue, 02 Aug 2022 16:42:20: 12000000 INFO @ Tue, 02 Aug 2022 16:42:22: 25000000 INFO @ Tue, 02 Aug 2022 16:42:23: 20000000 INFO @ Tue, 02 Aug 2022 16:42:27: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 16:42:27: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 16:42:27: #1 total tags in treatment: 25625387 INFO @ Tue, 02 Aug 2022 16:42:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:42:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:42:27: 13000000 INFO @ Tue, 02 Aug 2022 16:42:28: #1 tags after filtering in treatment: 25625386 INFO @ Tue, 02 Aug 2022 16:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:42:28: #1 finished! INFO @ Tue, 02 Aug 2022 16:42:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:42:30: #2 number of paired peaks: 598 WARNING @ Tue, 02 Aug 2022 16:42:30: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Tue, 02 Aug 2022 16:42:30: start model_add_line... INFO @ Tue, 02 Aug 2022 16:42:30: 21000000 INFO @ Tue, 02 Aug 2022 16:42:30: start X-correlation... INFO @ Tue, 02 Aug 2022 16:42:30: end of X-cor INFO @ Tue, 02 Aug 2022 16:42:30: #2 finished! INFO @ Tue, 02 Aug 2022 16:42:30: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 16:42:30: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 02 Aug 2022 16:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.05_model.r INFO @ Tue, 02 Aug 2022 16:42:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:42:35: 14000000 INFO @ Tue, 02 Aug 2022 16:42:36: 22000000 INFO @ Tue, 02 Aug 2022 16:42:42: 23000000 INFO @ Tue, 02 Aug 2022 16:42:43: 15000000 INFO @ Tue, 02 Aug 2022 16:42:48: 24000000 INFO @ Tue, 02 Aug 2022 16:42:51: 16000000 INFO @ Tue, 02 Aug 2022 16:42:54: 25000000 INFO @ Tue, 02 Aug 2022 16:42:58: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 16:42:58: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 16:42:58: #1 total tags in treatment: 25625387 INFO @ Tue, 02 Aug 2022 16:42:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:42:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:42:58: 17000000 INFO @ Tue, 02 Aug 2022 16:42:59: #1 tags after filtering in treatment: 25625386 INFO @ Tue, 02 Aug 2022 16:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:42:59: #1 finished! INFO @ Tue, 02 Aug 2022 16:42:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:43:01: #2 number of paired peaks: 598 WARNING @ Tue, 02 Aug 2022 16:43:01: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Tue, 02 Aug 2022 16:43:01: start model_add_line... INFO @ Tue, 02 Aug 2022 16:43:01: start X-correlation... INFO @ Tue, 02 Aug 2022 16:43:01: end of X-cor INFO @ Tue, 02 Aug 2022 16:43:01: #2 finished! INFO @ Tue, 02 Aug 2022 16:43:01: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 16:43:01: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 02 Aug 2022 16:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.10_model.r INFO @ Tue, 02 Aug 2022 16:43:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:43:06: 18000000 INFO @ Tue, 02 Aug 2022 16:43:13: 19000000 INFO @ Tue, 02 Aug 2022 16:43:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:43:21: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:43:30: 21000000 INFO @ Tue, 02 Aug 2022 16:43:38: 22000000 INFO @ Tue, 02 Aug 2022 16:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.05_summits.bed INFO @ Tue, 02 Aug 2022 16:43:41: Done! pass1 - making usageList (698 chroms): 3 millis pass2 - checking and writing primary data (12913 records, 4 fields): 113 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:43:46: 23000000 INFO @ Tue, 02 Aug 2022 16:43:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:43:53: 24000000 INFO @ Tue, 02 Aug 2022 16:44:00: 25000000 INFO @ Tue, 02 Aug 2022 16:44:06: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 16:44:06: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 16:44:06: #1 total tags in treatment: 25625387 INFO @ Tue, 02 Aug 2022 16:44:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:44:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:44:07: #1 tags after filtering in treatment: 25625386 INFO @ Tue, 02 Aug 2022 16:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:44:07: #1 finished! INFO @ Tue, 02 Aug 2022 16:44:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:44:08: #2 number of paired peaks: 598 WARNING @ Tue, 02 Aug 2022 16:44:08: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Tue, 02 Aug 2022 16:44:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:44:09: start X-correlation... INFO @ Tue, 02 Aug 2022 16:44:09: end of X-cor INFO @ Tue, 02 Aug 2022 16:44:09: #2 finished! INFO @ Tue, 02 Aug 2022 16:44:09: #2 predicted fragment length is 133 bps INFO @ Tue, 02 Aug 2022 16:44:09: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 02 Aug 2022 16:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.20_model.r INFO @ Tue, 02 Aug 2022 16:44:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:44:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.10_summits.bed INFO @ Tue, 02 Aug 2022 16:44:11: Done! pass1 - making usageList (610 chroms): 8 millis pass2 - checking and writing primary data (9233 records, 4 fields): 180 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:44:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8369900/SRX8369900.20_summits.bed INFO @ Tue, 02 Aug 2022 16:45:21: Done! pass1 - making usageList (455 chroms): 2 millis pass2 - checking and writing primary data (5613 records, 4 fields): 51 millis CompletedMACS2peakCalling