Job ID = 14172441 SRX = SRX3292998 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: 00:12:38 27740135 reads; of these: 27740135 (100.00%) were unpaired; of these: 804265 (2.90%) aligned 0 times 22600330 (81.47%) aligned exactly 1 time 4335540 (15.63%) aligned >1 times 97.10% overall alignment rate Time searching: 00:12:38 Overall time: 00:12:38 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] 2778055 / 26935870 = 0.1031 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.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 @ Sat, 11 Dec 2021 15:48:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:48:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:48:54: 1000000 INFO @ Sat, 11 Dec 2021 15:49:01: 2000000 INFO @ Sat, 11 Dec 2021 15:49:07: 3000000 INFO @ Sat, 11 Dec 2021 15:49:14: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.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 @ Sat, 11 Dec 2021 15:49:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:49:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:49:20: 5000000 INFO @ Sat, 11 Dec 2021 15:49:25: 1000000 INFO @ Sat, 11 Dec 2021 15:49:28: 6000000 INFO @ Sat, 11 Dec 2021 15:49:32: 2000000 INFO @ Sat, 11 Dec 2021 15:49:35: 7000000 INFO @ Sat, 11 Dec 2021 15:49:40: 3000000 INFO @ Sat, 11 Dec 2021 15:49:42: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:49:47: 4000000 INFO @ Sat, 11 Dec 2021 15:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.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 @ Sat, 11 Dec 2021 15:49:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:49:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:49:50: 9000000 INFO @ Sat, 11 Dec 2021 15:49:55: 5000000 INFO @ Sat, 11 Dec 2021 15:49:55: 1000000 INFO @ Sat, 11 Dec 2021 15:49:57: 10000000 INFO @ Sat, 11 Dec 2021 15:50:02: 6000000 INFO @ Sat, 11 Dec 2021 15:50:03: 2000000 INFO @ Sat, 11 Dec 2021 15:50:05: 11000000 INFO @ Sat, 11 Dec 2021 15:50:10: 7000000 INFO @ Sat, 11 Dec 2021 15:50:11: 3000000 INFO @ Sat, 11 Dec 2021 15:50:13: 12000000 INFO @ Sat, 11 Dec 2021 15:50:18: 8000000 INFO @ Sat, 11 Dec 2021 15:50:19: 4000000 INFO @ Sat, 11 Dec 2021 15:50:21: 13000000 INFO @ Sat, 11 Dec 2021 15:50:26: 9000000 INFO @ Sat, 11 Dec 2021 15:50:27: 5000000 INFO @ Sat, 11 Dec 2021 15:50:29: 14000000 INFO @ Sat, 11 Dec 2021 15:50:33: 10000000 INFO @ Sat, 11 Dec 2021 15:50:34: 6000000 INFO @ Sat, 11 Dec 2021 15:50:37: 15000000 INFO @ Sat, 11 Dec 2021 15:50:41: 11000000 INFO @ Sat, 11 Dec 2021 15:50:42: 7000000 INFO @ Sat, 11 Dec 2021 15:50:44: 16000000 INFO @ Sat, 11 Dec 2021 15:50:49: 12000000 INFO @ Sat, 11 Dec 2021 15:50:50: 8000000 INFO @ Sat, 11 Dec 2021 15:50:52: 17000000 INFO @ Sat, 11 Dec 2021 15:50:56: 13000000 INFO @ Sat, 11 Dec 2021 15:50:58: 9000000 INFO @ Sat, 11 Dec 2021 15:51:00: 18000000 INFO @ Sat, 11 Dec 2021 15:51:04: 14000000 INFO @ Sat, 11 Dec 2021 15:51:05: 10000000 INFO @ Sat, 11 Dec 2021 15:51:07: 19000000 INFO @ Sat, 11 Dec 2021 15:51:12: 15000000 INFO @ Sat, 11 Dec 2021 15:51:13: 11000000 INFO @ Sat, 11 Dec 2021 15:51:16: 20000000 INFO @ Sat, 11 Dec 2021 15:51:19: 16000000 INFO @ Sat, 11 Dec 2021 15:51:20: 12000000 INFO @ Sat, 11 Dec 2021 15:51:23: 21000000 INFO @ Sat, 11 Dec 2021 15:51:27: 17000000 INFO @ Sat, 11 Dec 2021 15:51:28: 13000000 INFO @ Sat, 11 Dec 2021 15:51:31: 22000000 INFO @ Sat, 11 Dec 2021 15:51:34: 18000000 INFO @ Sat, 11 Dec 2021 15:51:36: 14000000 INFO @ Sat, 11 Dec 2021 15:51:39: 23000000 INFO @ Sat, 11 Dec 2021 15:51:42: 19000000 INFO @ Sat, 11 Dec 2021 15:51:43: 15000000 INFO @ Sat, 11 Dec 2021 15:51:46: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:51:48: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:51:48: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:51:48: #1 total tags in treatment: 24157815 INFO @ Sat, 11 Dec 2021 15:51:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:51:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:51:48: #1 tags after filtering in treatment: 24157644 INFO @ Sat, 11 Dec 2021 15:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:51:48: #1 finished! INFO @ Sat, 11 Dec 2021 15:51:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:51:50: 20000000 INFO @ Sat, 11 Dec 2021 15:51:50: #2 number of paired peaks: 228 WARNING @ Sat, 11 Dec 2021 15:51:50: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sat, 11 Dec 2021 15:51:50: start model_add_line... INFO @ Sat, 11 Dec 2021 15:51:50: start X-correlation... INFO @ Sat, 11 Dec 2021 15:51:50: end of X-cor INFO @ Sat, 11 Dec 2021 15:51:50: #2 finished! INFO @ Sat, 11 Dec 2021 15:51:50: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 15:51:50: #2 alternative fragment length(s) may be 1,94 bps INFO @ Sat, 11 Dec 2021 15:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.05_model.r WARNING @ Sat, 11 Dec 2021 15:51:50: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:51:50: #2 You may need to consider one of the other alternative d(s): 1,94 WARNING @ Sat, 11 Dec 2021 15:51:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:51:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:51:51: 16000000 INFO @ Sat, 11 Dec 2021 15:51:57: 21000000 INFO @ Sat, 11 Dec 2021 15:51:58: 17000000 INFO @ Sat, 11 Dec 2021 15:52:05: 22000000 INFO @ Sat, 11 Dec 2021 15:52:06: 18000000 INFO @ Sat, 11 Dec 2021 15:52:12: 23000000 INFO @ Sat, 11 Dec 2021 15:52:13: 19000000 INFO @ Sat, 11 Dec 2021 15:52:20: 24000000 INFO @ Sat, 11 Dec 2021 15:52:21: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:52:21: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:52:21: #1 total tags in treatment: 24157815 INFO @ Sat, 11 Dec 2021 15:52:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:52:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:52:21: 20000000 INFO @ Sat, 11 Dec 2021 15:52:22: #1 tags after filtering in treatment: 24157644 INFO @ Sat, 11 Dec 2021 15:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:52:22: #1 finished! INFO @ Sat, 11 Dec 2021 15:52:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:52:23: #2 number of paired peaks: 228 WARNING @ Sat, 11 Dec 2021 15:52:23: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sat, 11 Dec 2021 15:52:23: start model_add_line... INFO @ Sat, 11 Dec 2021 15:52:23: start X-correlation... INFO @ Sat, 11 Dec 2021 15:52:23: end of X-cor INFO @ Sat, 11 Dec 2021 15:52:23: #2 finished! INFO @ Sat, 11 Dec 2021 15:52:23: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 15:52:23: #2 alternative fragment length(s) may be 1,94 bps INFO @ Sat, 11 Dec 2021 15:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.10_model.r WARNING @ Sat, 11 Dec 2021 15:52:23: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:52:23: #2 You may need to consider one of the other alternative d(s): 1,94 WARNING @ Sat, 11 Dec 2021 15:52:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:52:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:52:28: 21000000 INFO @ Sat, 11 Dec 2021 15:52:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:52:35: 22000000 INFO @ Sat, 11 Dec 2021 15:52:42: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:52:48: 24000000 INFO @ Sat, 11 Dec 2021 15:52:50: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:52:50: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:52:50: #1 total tags in treatment: 24157815 INFO @ Sat, 11 Dec 2021 15:52:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:52:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:52:50: #1 tags after filtering in treatment: 24157644 INFO @ Sat, 11 Dec 2021 15:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:52:50: #1 finished! INFO @ Sat, 11 Dec 2021 15:52:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:52:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:52:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:52:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.05_summits.bed INFO @ Sat, 11 Dec 2021 15:52:51: Done! pass1 - making usageList (428 chroms): 1 millis pass2 - checking and writing primary data (1270 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:52:52: #2 number of paired peaks: 228 WARNING @ Sat, 11 Dec 2021 15:52:52: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sat, 11 Dec 2021 15:52:52: start model_add_line... INFO @ Sat, 11 Dec 2021 15:52:52: start X-correlation... INFO @ Sat, 11 Dec 2021 15:52:52: end of X-cor INFO @ Sat, 11 Dec 2021 15:52:52: #2 finished! INFO @ Sat, 11 Dec 2021 15:52:52: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 15:52:52: #2 alternative fragment length(s) may be 1,94 bps INFO @ Sat, 11 Dec 2021 15:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.20_model.r WARNING @ Sat, 11 Dec 2021 15:52:52: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:52:52: #2 You may need to consider one of the other alternative d(s): 1,94 WARNING @ Sat, 11 Dec 2021 15:52:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:52:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:53:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.10_summits.bed INFO @ Sat, 11 Dec 2021 15:53:23: Done! pass1 - making usageList (351 chroms): 2 millis pass2 - checking and writing primary data (836 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:53:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292998/SRX3292998.20_summits.bed INFO @ Sat, 11 Dec 2021 15:53:51: Done! pass1 - making usageList (220 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 19 millis CompletedMACS2peakCalling