Job ID = 6529529 SRX = SRX287946 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: 00:00:01 Multiseed full-index search: 00:08:30 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1437518 (5.34%) aligned 0 times 17200716 (63.89%) aligned exactly 1 time 8285994 (30.78%) aligned >1 times 94.66% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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] 4922286 / 25486710 = 0.1931 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 02:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.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 02:24:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:59: 1000000 INFO @ Tue, 30 Jun 2020 02:25:05: 2000000 INFO @ Tue, 30 Jun 2020 02:25:11: 3000000 INFO @ Tue, 30 Jun 2020 02:25:16: 4000000 INFO @ Tue, 30 Jun 2020 02:25:22: 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 02:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.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 02:25:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:28: 6000000 INFO @ Tue, 30 Jun 2020 02:25:30: 1000000 INFO @ Tue, 30 Jun 2020 02:25:34: 7000000 INFO @ Tue, 30 Jun 2020 02:25:38: 2000000 INFO @ Tue, 30 Jun 2020 02:25:41: 8000000 INFO @ Tue, 30 Jun 2020 02:25:44: 3000000 INFO @ Tue, 30 Jun 2020 02:25:47: 9000000 INFO @ Tue, 30 Jun 2020 02:25:51: 4000000 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 02:25:53: 10000000 INFO @ Tue, 30 Jun 2020 02:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.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 02:25:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:58: 5000000 INFO @ Tue, 30 Jun 2020 02:26:00: 11000000 INFO @ Tue, 30 Jun 2020 02:26:00: 1000000 INFO @ Tue, 30 Jun 2020 02:26:04: 6000000 INFO @ Tue, 30 Jun 2020 02:26:06: 12000000 INFO @ Tue, 30 Jun 2020 02:26:07: 2000000 INFO @ Tue, 30 Jun 2020 02:26:11: 7000000 INFO @ Tue, 30 Jun 2020 02:26:13: 13000000 INFO @ Tue, 30 Jun 2020 02:26:14: 3000000 INFO @ Tue, 30 Jun 2020 02:26:17: 8000000 INFO @ Tue, 30 Jun 2020 02:26:19: 14000000 INFO @ Tue, 30 Jun 2020 02:26:20: 4000000 INFO @ Tue, 30 Jun 2020 02:26:24: 9000000 INFO @ Tue, 30 Jun 2020 02:26:26: 15000000 INFO @ Tue, 30 Jun 2020 02:26:27: 5000000 INFO @ Tue, 30 Jun 2020 02:26:30: 10000000 INFO @ Tue, 30 Jun 2020 02:26:32: 16000000 INFO @ Tue, 30 Jun 2020 02:26:34: 6000000 INFO @ Tue, 30 Jun 2020 02:26:36: 11000000 INFO @ Tue, 30 Jun 2020 02:26:39: 17000000 INFO @ Tue, 30 Jun 2020 02:26:40: 7000000 INFO @ Tue, 30 Jun 2020 02:26:42: 12000000 INFO @ Tue, 30 Jun 2020 02:26:46: 18000000 INFO @ Tue, 30 Jun 2020 02:26:47: 8000000 INFO @ Tue, 30 Jun 2020 02:26:49: 13000000 INFO @ Tue, 30 Jun 2020 02:26:52: 19000000 INFO @ Tue, 30 Jun 2020 02:26:53: 9000000 INFO @ Tue, 30 Jun 2020 02:26:55: 14000000 INFO @ Tue, 30 Jun 2020 02:26:59: 20000000 INFO @ Tue, 30 Jun 2020 02:26:59: 10000000 INFO @ Tue, 30 Jun 2020 02:27:02: 15000000 INFO @ Tue, 30 Jun 2020 02:27:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:03: #1 total tags in treatment: 20564424 INFO @ Tue, 30 Jun 2020 02:27:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:03: #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 02:27:03: #1 tags after filtering in treatment: 20564424 INFO @ Tue, 30 Jun 2020 02:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:05: #2 number of paired peaks: 566 WARNING @ Tue, 30 Jun 2020 02:27:05: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:05: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:27:05: #2 alternative fragment length(s) may be 2,21,589,596 bps INFO @ Tue, 30 Jun 2020 02:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.05_model.r WARNING @ Tue, 30 Jun 2020 02:27:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:05: #2 You may need to consider one of the other alternative d(s): 2,21,589,596 WARNING @ Tue, 30 Jun 2020 02:27:05: #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 02:27:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:06: 11000000 INFO @ Tue, 30 Jun 2020 02:27:08: 16000000 INFO @ Tue, 30 Jun 2020 02:27:12: 12000000 INFO @ Tue, 30 Jun 2020 02:27:15: 17000000 INFO @ Tue, 30 Jun 2020 02:27:18: 13000000 INFO @ Tue, 30 Jun 2020 02:27:21: 18000000 INFO @ Tue, 30 Jun 2020 02:27:24: 14000000 INFO @ Tue, 30 Jun 2020 02:27:28: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:27:31: 15000000 INFO @ Tue, 30 Jun 2020 02:27:34: 20000000 INFO @ Tue, 30 Jun 2020 02:27:37: 16000000 INFO @ Tue, 30 Jun 2020 02:27:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:38: #1 total tags in treatment: 20564424 INFO @ Tue, 30 Jun 2020 02:27:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:38: #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 02:27:39: #1 tags after filtering in treatment: 20564424 INFO @ Tue, 30 Jun 2020 02:27:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:40: #2 number of paired peaks: 566 WARNING @ Tue, 30 Jun 2020 02:27:40: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:40: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:27:40: #2 alternative fragment length(s) may be 2,21,589,596 bps INFO @ Tue, 30 Jun 2020 02:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.10_model.r WARNING @ Tue, 30 Jun 2020 02:27:40: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:40: #2 You may need to consider one of the other alternative d(s): 2,21,589,596 WARNING @ Tue, 30 Jun 2020 02:27:40: #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 02:27:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:43: 17000000 INFO @ Tue, 30 Jun 2020 02:27:49: 18000000 INFO @ Tue, 30 Jun 2020 02:27:55: 19000000 INFO @ Tue, 30 Jun 2020 02:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.05_summits.bed INFO @ Tue, 30 Jun 2020 02:28:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:28:01: 20000000 INFO @ Tue, 30 Jun 2020 02:28:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:04: #1 total tags in treatment: 20564424 INFO @ Tue, 30 Jun 2020 02:28:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:04: #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 02:28:05: #1 tags after filtering in treatment: 20564424 INFO @ Tue, 30 Jun 2020 02:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:07: #2 number of paired peaks: 566 WARNING @ Tue, 30 Jun 2020 02:28:07: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:07: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:28:07: #2 alternative fragment length(s) may be 2,21,589,596 bps INFO @ Tue, 30 Jun 2020 02:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.20_model.r WARNING @ Tue, 30 Jun 2020 02:28:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:07: #2 You may need to consider one of the other alternative d(s): 2,21,589,596 WARNING @ Tue, 30 Jun 2020 02:28:07: #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 02:28:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:28:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.10_summits.bed INFO @ Tue, 30 Jun 2020 02:28:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:28:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287946/SRX287946.20_summits.bed INFO @ Tue, 30 Jun 2020 02:29:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling