Job ID = 6529749 SRX = SRX4669056 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: 00:07:02 27136641 reads; of these: 27136641 (100.00%) were unpaired; of these: 1594760 (5.88%) aligned 0 times 22044861 (81.24%) aligned exactly 1 time 3497020 (12.89%) aligned >1 times 94.12% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 4885159 / 25541881 = 0.1913 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 02:51:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.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 02:51:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:29: 1000000 INFO @ Tue, 30 Jun 2020 02:51:34: 2000000 INFO @ Tue, 30 Jun 2020 02:51:40: 3000000 INFO @ Tue, 30 Jun 2020 02:51:45: 4000000 INFO @ Tue, 30 Jun 2020 02:51:50: 5000000 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 02:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.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 02:51:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:56: 6000000 INFO @ Tue, 30 Jun 2020 02:51:59: 1000000 INFO @ Tue, 30 Jun 2020 02:52:02: 7000000 INFO @ Tue, 30 Jun 2020 02:52:05: 2000000 INFO @ Tue, 30 Jun 2020 02:52:08: 8000000 INFO @ Tue, 30 Jun 2020 02:52:11: 3000000 INFO @ Tue, 30 Jun 2020 02:52:14: 9000000 INFO @ Tue, 30 Jun 2020 02:52:18: 4000000 INFO @ Tue, 30 Jun 2020 02:52:20: 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 02:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.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 02:52:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:24: 5000000 INFO @ Tue, 30 Jun 2020 02:52:26: 11000000 INFO @ Tue, 30 Jun 2020 02:52:29: 1000000 INFO @ Tue, 30 Jun 2020 02:52:30: 6000000 INFO @ Tue, 30 Jun 2020 02:52:32: 12000000 INFO @ Tue, 30 Jun 2020 02:52:34: 2000000 INFO @ Tue, 30 Jun 2020 02:52:36: 7000000 INFO @ Tue, 30 Jun 2020 02:52:38: 13000000 INFO @ Tue, 30 Jun 2020 02:52:40: 3000000 INFO @ Tue, 30 Jun 2020 02:52:43: 8000000 INFO @ Tue, 30 Jun 2020 02:52:44: 14000000 INFO @ Tue, 30 Jun 2020 02:52:46: 4000000 INFO @ Tue, 30 Jun 2020 02:52:49: 9000000 INFO @ Tue, 30 Jun 2020 02:52:50: 15000000 INFO @ Tue, 30 Jun 2020 02:52:51: 5000000 INFO @ Tue, 30 Jun 2020 02:52:55: 10000000 INFO @ Tue, 30 Jun 2020 02:52:57: 16000000 INFO @ Tue, 30 Jun 2020 02:52:57: 6000000 INFO @ Tue, 30 Jun 2020 02:53:01: 11000000 INFO @ Tue, 30 Jun 2020 02:53:03: 7000000 INFO @ Tue, 30 Jun 2020 02:53:03: 17000000 INFO @ Tue, 30 Jun 2020 02:53:08: 12000000 INFO @ Tue, 30 Jun 2020 02:53:08: 8000000 INFO @ Tue, 30 Jun 2020 02:53:09: 18000000 INFO @ Tue, 30 Jun 2020 02:53:13: 13000000 INFO @ Tue, 30 Jun 2020 02:53:14: 9000000 INFO @ Tue, 30 Jun 2020 02:53:15: 19000000 INFO @ Tue, 30 Jun 2020 02:53:19: 14000000 INFO @ Tue, 30 Jun 2020 02:53:19: 10000000 INFO @ Tue, 30 Jun 2020 02:53:21: 20000000 INFO @ Tue, 30 Jun 2020 02:53:25: 15000000 INFO @ Tue, 30 Jun 2020 02:53:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:25: #1 total tags in treatment: 20656722 INFO @ Tue, 30 Jun 2020 02:53:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:25: #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 02:53:25: 11000000 INFO @ Tue, 30 Jun 2020 02:53:26: #1 tags after filtering in treatment: 20656718 INFO @ Tue, 30 Jun 2020 02:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:27: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 02:53:27: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:27: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:53:27: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 02:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.05_model.r WARNING @ Tue, 30 Jun 2020 02:53:27: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:27: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 02:53:27: #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 02:53:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:30: 16000000 INFO @ Tue, 30 Jun 2020 02:53:30: 12000000 INFO @ Tue, 30 Jun 2020 02:53:36: 13000000 INFO @ Tue, 30 Jun 2020 02:53:36: 17000000 INFO @ Tue, 30 Jun 2020 02:53:41: 14000000 INFO @ Tue, 30 Jun 2020 02:53:42: 18000000 INFO @ Tue, 30 Jun 2020 02:53:47: 15000000 INFO @ Tue, 30 Jun 2020 02:53:47: 19000000 INFO @ Tue, 30 Jun 2020 02:53:52: 16000000 INFO @ Tue, 30 Jun 2020 02:53:53: 20000000 INFO @ Tue, 30 Jun 2020 02:53:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:57: #1 total tags in treatment: 20656722 INFO @ Tue, 30 Jun 2020 02:53:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:57: #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 02:53:57: #1 tags after filtering in treatment: 20656718 INFO @ Tue, 30 Jun 2020 02:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:58: 17000000 INFO @ Tue, 30 Jun 2020 02:53:59: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 02:53:59: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:59: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:53:59: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 02:53:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.10_model.r WARNING @ Tue, 30 Jun 2020 02:53:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:59: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 02:53:59: #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 02:53:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:03: 18000000 INFO @ Tue, 30 Jun 2020 02:54:09: 19000000 INFO @ Tue, 30 Jun 2020 02:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:14: 20000000 INFO @ Tue, 30 Jun 2020 02:54:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:18: #1 total tags in treatment: 20656722 INFO @ Tue, 30 Jun 2020 02:54:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:18: #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 02:54:18: #1 tags after filtering in treatment: 20656718 INFO @ Tue, 30 Jun 2020 02:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:20: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 02:54:20: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:20: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:54:20: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 02:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.20_model.r WARNING @ Tue, 30 Jun 2020 02:54:20: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:20: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 02:54:20: #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 02:54:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.05_summits.bed INFO @ Tue, 30 Jun 2020 02:54:32: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (2437 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:54:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.10_summits.bed INFO @ Tue, 30 Jun 2020 02:55:02: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669056/SRX4669056.20_summits.bed INFO @ Tue, 30 Jun 2020 02:55:24: Done! pass1 - making usageList (155 chroms): 1 millis pass2 - checking and writing primary data (271 records, 4 fields): 8 millis CompletedMACS2peakCalling