Job ID = 16438965 SRX = SRX10031695 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:02 31828133 reads; of these: 31828133 (100.00%) were unpaired; of these: 928568 (2.92%) aligned 0 times 25269662 (79.39%) aligned exactly 1 time 5629903 (17.69%) aligned >1 times 97.08% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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] 6494049 / 30899565 = 0.2102 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 14:38:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.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 14:38:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:38:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:38:49: 1000000 INFO @ Tue, 02 Aug 2022 14:38:57: 2000000 INFO @ Tue, 02 Aug 2022 14:39:04: 3000000 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 14:39:11: 4000000 INFO @ Tue, 02 Aug 2022 14:39:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.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 14:39:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:39:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:20: 5000000 INFO @ Tue, 02 Aug 2022 14:39:21: 1000000 INFO @ Tue, 02 Aug 2022 14:39:28: 6000000 INFO @ Tue, 02 Aug 2022 14:39:30: 2000000 INFO @ Tue, 02 Aug 2022 14:39:36: 7000000 INFO @ Tue, 02 Aug 2022 14:39:39: 3000000 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 14:39:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.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 14:39:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:39:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:44: 8000000 INFO @ Tue, 02 Aug 2022 14:39:48: 4000000 INFO @ Tue, 02 Aug 2022 14:39:50: 1000000 INFO @ Tue, 02 Aug 2022 14:39:53: 9000000 INFO @ Tue, 02 Aug 2022 14:39:56: 5000000 INFO @ Tue, 02 Aug 2022 14:39:58: 2000000 INFO @ Tue, 02 Aug 2022 14:40:02: 10000000 INFO @ Tue, 02 Aug 2022 14:40:05: 6000000 INFO @ Tue, 02 Aug 2022 14:40:05: 3000000 INFO @ Tue, 02 Aug 2022 14:40:11: 11000000 INFO @ Tue, 02 Aug 2022 14:40:13: 4000000 INFO @ Tue, 02 Aug 2022 14:40:14: 7000000 INFO @ Tue, 02 Aug 2022 14:40:20: 12000000 INFO @ Tue, 02 Aug 2022 14:40:21: 5000000 INFO @ Tue, 02 Aug 2022 14:40:23: 8000000 INFO @ Tue, 02 Aug 2022 14:40:28: 6000000 INFO @ Tue, 02 Aug 2022 14:40:29: 13000000 INFO @ Tue, 02 Aug 2022 14:40:32: 9000000 INFO @ Tue, 02 Aug 2022 14:40:36: 7000000 INFO @ Tue, 02 Aug 2022 14:40:38: 14000000 INFO @ Tue, 02 Aug 2022 14:40:41: 10000000 INFO @ Tue, 02 Aug 2022 14:40:43: 8000000 INFO @ Tue, 02 Aug 2022 14:40:47: 15000000 INFO @ Tue, 02 Aug 2022 14:40:49: 11000000 INFO @ Tue, 02 Aug 2022 14:40:50: 9000000 INFO @ Tue, 02 Aug 2022 14:40:56: 16000000 INFO @ Tue, 02 Aug 2022 14:40:57: 10000000 INFO @ Tue, 02 Aug 2022 14:40:58: 12000000 INFO @ Tue, 02 Aug 2022 14:41:04: 11000000 INFO @ Tue, 02 Aug 2022 14:41:04: 17000000 INFO @ Tue, 02 Aug 2022 14:41:07: 13000000 INFO @ Tue, 02 Aug 2022 14:41:11: 12000000 INFO @ Tue, 02 Aug 2022 14:41:13: 18000000 INFO @ Tue, 02 Aug 2022 14:41:15: 14000000 INFO @ Tue, 02 Aug 2022 14:41:18: 13000000 INFO @ Tue, 02 Aug 2022 14:41:21: 19000000 INFO @ Tue, 02 Aug 2022 14:41:24: 15000000 INFO @ Tue, 02 Aug 2022 14:41:25: 14000000 INFO @ Tue, 02 Aug 2022 14:41:31: 20000000 INFO @ Tue, 02 Aug 2022 14:41:33: 16000000 INFO @ Tue, 02 Aug 2022 14:41:33: 15000000 INFO @ Tue, 02 Aug 2022 14:41:40: 16000000 INFO @ Tue, 02 Aug 2022 14:41:40: 21000000 INFO @ Tue, 02 Aug 2022 14:41:41: 17000000 INFO @ Tue, 02 Aug 2022 14:41:48: 17000000 INFO @ Tue, 02 Aug 2022 14:41:49: 22000000 INFO @ Tue, 02 Aug 2022 14:41:50: 18000000 INFO @ Tue, 02 Aug 2022 14:41:56: 18000000 INFO @ Tue, 02 Aug 2022 14:41:57: 23000000 INFO @ Tue, 02 Aug 2022 14:41:59: 19000000 INFO @ Tue, 02 Aug 2022 14:42:03: 19000000 INFO @ Tue, 02 Aug 2022 14:42:06: 24000000 INFO @ Tue, 02 Aug 2022 14:42:09: 20000000 INFO @ Tue, 02 Aug 2022 14:42:10: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:42:10: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:42:10: #1 total tags in treatment: 24405516 INFO @ Tue, 02 Aug 2022 14:42:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:10: #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 14:42:11: #1 tags after filtering in treatment: 24405425 INFO @ Tue, 02 Aug 2022 14:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:11: 20000000 INFO @ Tue, 02 Aug 2022 14:42:13: #2 number of paired peaks: 242 WARNING @ Tue, 02 Aug 2022 14:42:13: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 02 Aug 2022 14:42:13: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:13: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:13: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:13: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:13: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 14:42:13: #2 alternative fragment length(s) may be 1,25,42,68 bps INFO @ Tue, 02 Aug 2022 14:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.05_model.r WARNING @ Tue, 02 Aug 2022 14:42:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:13: #2 You may need to consider one of the other alternative d(s): 1,25,42,68 WARNING @ Tue, 02 Aug 2022 14:42:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:42:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:42:17: 21000000 INFO @ Tue, 02 Aug 2022 14:42:18: 21000000 INFO @ Tue, 02 Aug 2022 14:42:25: 22000000 INFO @ Tue, 02 Aug 2022 14:42:25: 22000000 INFO @ Tue, 02 Aug 2022 14:42:33: 23000000 INFO @ Tue, 02 Aug 2022 14:42:33: 23000000 INFO @ Tue, 02 Aug 2022 14:42:40: 24000000 INFO @ Tue, 02 Aug 2022 14:42:41: 24000000 INFO @ Tue, 02 Aug 2022 14:42:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:42:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:42:43: #1 total tags in treatment: 24405516 INFO @ Tue, 02 Aug 2022 14:42:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:43: #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 14:42:44: #1 tags after filtering in treatment: 24405425 INFO @ Tue, 02 Aug 2022 14:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:44: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:42:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:42:44: #1 total tags in treatment: 24405516 INFO @ Tue, 02 Aug 2022 14:42:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:44: #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 14:42:45: #1 tags after filtering in treatment: 24405425 INFO @ Tue, 02 Aug 2022 14:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:46: #2 number of paired peaks: 242 WARNING @ Tue, 02 Aug 2022 14:42:46: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 02 Aug 2022 14:42:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:46: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 14:42:46: #2 alternative fragment length(s) may be 1,25,42,68 bps INFO @ Tue, 02 Aug 2022 14:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.20_model.r WARNING @ Tue, 02 Aug 2022 14:42:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:46: #2 You may need to consider one of the other alternative d(s): 1,25,42,68 WARNING @ Tue, 02 Aug 2022 14:42:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:42:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:47: #2 number of paired peaks: 242 WARNING @ Tue, 02 Aug 2022 14:42:47: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Tue, 02 Aug 2022 14:42:47: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:47: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:47: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:47: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:47: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 14:42:47: #2 alternative fragment length(s) may be 1,25,42,68 bps INFO @ Tue, 02 Aug 2022 14:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.10_model.r WARNING @ Tue, 02 Aug 2022 14:42:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:47: #2 You may need to consider one of the other alternative d(s): 1,25,42,68 WARNING @ Tue, 02 Aug 2022 14:42:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:42:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.05_summits.bed INFO @ Tue, 02 Aug 2022 14:43:06: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:43:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:43:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.20_summits.bed INFO @ Tue, 02 Aug 2022 14:43:39: Done! INFO @ Tue, 02 Aug 2022 14:43:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031695/SRX10031695.10_summits.bed INFO @ Tue, 02 Aug 2022 14:43:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling