Job ID = 6529367 SRX = SRX2068663 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: 00:07:52 53411613 reads; of these: 53411613 (100.00%) were unpaired; of these: 19168065 (35.89%) aligned 0 times 26303166 (49.25%) aligned exactly 1 time 7940382 (14.87%) aligned >1 times 64.11% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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] 12197321 / 34243548 = 0.3562 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 01:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.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 01:55:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:55:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:55:54: 1000000 INFO @ Tue, 30 Jun 2020 01:55:59: 2000000 INFO @ Tue, 30 Jun 2020 01:56:05: 3000000 INFO @ Tue, 30 Jun 2020 01:56:11: 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 01:56:16: 5000000 INFO @ Tue, 30 Jun 2020 01:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.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 01:56:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:22: 6000000 INFO @ Tue, 30 Jun 2020 01:56:24: 1000000 INFO @ Tue, 30 Jun 2020 01:56:28: 7000000 INFO @ Tue, 30 Jun 2020 01:56:30: 2000000 INFO @ Tue, 30 Jun 2020 01:56:33: 8000000 INFO @ Tue, 30 Jun 2020 01:56:35: 3000000 INFO @ Tue, 30 Jun 2020 01:56:39: 9000000 INFO @ Tue, 30 Jun 2020 01:56:41: 4000000 INFO @ Tue, 30 Jun 2020 01:56:44: 10000000 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 01:56:47: 5000000 INFO @ Tue, 30 Jun 2020 01:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.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 01:56:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:50: 11000000 INFO @ Tue, 30 Jun 2020 01:56:53: 6000000 INFO @ Tue, 30 Jun 2020 01:56:54: 1000000 INFO @ Tue, 30 Jun 2020 01:56:56: 12000000 INFO @ Tue, 30 Jun 2020 01:56:59: 7000000 INFO @ Tue, 30 Jun 2020 01:57:00: 2000000 INFO @ Tue, 30 Jun 2020 01:57:01: 13000000 INFO @ Tue, 30 Jun 2020 01:57:04: 8000000 INFO @ Tue, 30 Jun 2020 01:57:06: 3000000 INFO @ Tue, 30 Jun 2020 01:57:07: 14000000 INFO @ Tue, 30 Jun 2020 01:57:10: 9000000 INFO @ Tue, 30 Jun 2020 01:57:12: 4000000 INFO @ Tue, 30 Jun 2020 01:57:13: 15000000 INFO @ Tue, 30 Jun 2020 01:57:16: 10000000 INFO @ Tue, 30 Jun 2020 01:57:18: 5000000 INFO @ Tue, 30 Jun 2020 01:57:18: 16000000 INFO @ Tue, 30 Jun 2020 01:57:21: 11000000 INFO @ Tue, 30 Jun 2020 01:57:24: 17000000 INFO @ Tue, 30 Jun 2020 01:57:24: 6000000 INFO @ Tue, 30 Jun 2020 01:57:27: 12000000 INFO @ Tue, 30 Jun 2020 01:57:30: 7000000 INFO @ Tue, 30 Jun 2020 01:57:30: 18000000 INFO @ Tue, 30 Jun 2020 01:57:33: 13000000 INFO @ Tue, 30 Jun 2020 01:57:36: 8000000 INFO @ Tue, 30 Jun 2020 01:57:36: 19000000 INFO @ Tue, 30 Jun 2020 01:57:38: 14000000 INFO @ Tue, 30 Jun 2020 01:57:41: 9000000 INFO @ Tue, 30 Jun 2020 01:57:41: 20000000 INFO @ Tue, 30 Jun 2020 01:57:44: 15000000 INFO @ Tue, 30 Jun 2020 01:57:47: 21000000 INFO @ Tue, 30 Jun 2020 01:57:47: 10000000 INFO @ Tue, 30 Jun 2020 01:57:50: 16000000 INFO @ Tue, 30 Jun 2020 01:57:53: 11000000 INFO @ Tue, 30 Jun 2020 01:57:53: 22000000 INFO @ Tue, 30 Jun 2020 01:57:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:57:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:57:53: #1 total tags in treatment: 22046227 INFO @ Tue, 30 Jun 2020 01:57:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:53: #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 01:57:54: #1 tags after filtering in treatment: 22046155 INFO @ Tue, 30 Jun 2020 01:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:54: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:55: 17000000 INFO @ Tue, 30 Jun 2020 01:57:56: #2 number of paired peaks: 600 WARNING @ Tue, 30 Jun 2020 01:57:56: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:56: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 01:57:56: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 30 Jun 2020 01:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:56: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:56: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 30 Jun 2020 01:57:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:57:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:58: 12000000 INFO @ Tue, 30 Jun 2020 01:58:01: 18000000 INFO @ Tue, 30 Jun 2020 01:58:04: 13000000 INFO @ Tue, 30 Jun 2020 01:58:07: 19000000 INFO @ Tue, 30 Jun 2020 01:58:10: 14000000 INFO @ Tue, 30 Jun 2020 01:58:13: 20000000 INFO @ Tue, 30 Jun 2020 01:58:16: 15000000 INFO @ Tue, 30 Jun 2020 01:58:18: 21000000 INFO @ Tue, 30 Jun 2020 01:58:21: 16000000 INFO @ Tue, 30 Jun 2020 01:58:24: 22000000 INFO @ Tue, 30 Jun 2020 01:58:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:58:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:58:25: #1 total tags in treatment: 22046227 INFO @ Tue, 30 Jun 2020 01:58:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:25: #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 01:58:25: #1 tags after filtering in treatment: 22046155 INFO @ Tue, 30 Jun 2020 01:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:25: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:27: #2 number of paired peaks: 600 WARNING @ Tue, 30 Jun 2020 01:58:27: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:27: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:27: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:27: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 01:58:27: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 30 Jun 2020 01:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.10_model.r WARNING @ Tue, 30 Jun 2020 01:58:27: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:27: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 30 Jun 2020 01:58:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:27: 17000000 INFO @ Tue, 30 Jun 2020 01:58:33: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:58:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:39: 19000000 INFO @ Tue, 30 Jun 2020 01:58:44: 20000000 INFO @ Tue, 30 Jun 2020 01:58:50: 21000000 INFO @ Tue, 30 Jun 2020 01:58:56: 22000000 INFO @ Tue, 30 Jun 2020 01:58:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:58:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:58:56: #1 total tags in treatment: 22046227 INFO @ Tue, 30 Jun 2020 01:58:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:56: #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 01:58:57: #1 tags after filtering in treatment: 22046155 INFO @ Tue, 30 Jun 2020 01:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:57: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:58: #2 number of paired peaks: 600 WARNING @ Tue, 30 Jun 2020 01:58:58: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:58: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:58: Done! INFO @ Tue, 30 Jun 2020 01:58:59: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:59: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:59: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:59: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 01:58:59: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 30 Jun 2020 01:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:59: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:59: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 30 Jun 2020 01:58:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:59: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (645 chroms): 2 millis pass2 - checking and writing primary data (3129 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.10_summits.bed INFO @ Tue, 30 Jun 2020 01:59:29: Done! pass1 - making usageList (561 chroms): 2 millis pass2 - checking and writing primary data (2436 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:59:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2068663/SRX2068663.20_summits.bed INFO @ Tue, 30 Jun 2020 02:00:03: Done! pass1 - making usageList (421 chroms): 1 millis pass2 - checking and writing primary data (1267 records, 4 fields): 14 millis CompletedMACS2peakCalling