Job ID = 6529208 SRX = SRX041399 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: 00:06:01 26182829 reads; of these: 26182829 (100.00%) were unpaired; of these: 1473431 (5.63%) aligned 0 times 18974196 (72.47%) aligned exactly 1 time 5735202 (21.90%) aligned >1 times 94.37% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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 8 files... [bam_rmdupse_core] 3224047 / 24709398 = 0.1305 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 01:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.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 01:34:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:34:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:34:20: 1000000 INFO @ Tue, 30 Jun 2020 01:34:25: 2000000 INFO @ Tue, 30 Jun 2020 01:34:31: 3000000 INFO @ Tue, 30 Jun 2020 01:34:36: 4000000 INFO @ Tue, 30 Jun 2020 01:34:41: 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 01:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.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 01:34:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:34:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:34:47: 6000000 INFO @ Tue, 30 Jun 2020 01:34:50: 1000000 INFO @ Tue, 30 Jun 2020 01:34:52: 7000000 INFO @ Tue, 30 Jun 2020 01:34:56: 2000000 INFO @ Tue, 30 Jun 2020 01:34:58: 8000000 INFO @ Tue, 30 Jun 2020 01:35:02: 3000000 INFO @ Tue, 30 Jun 2020 01:35:04: 9000000 INFO @ Tue, 30 Jun 2020 01:35:08: 4000000 INFO @ Tue, 30 Jun 2020 01:35:10: 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 01:35:14: 5000000 INFO @ Tue, 30 Jun 2020 01:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.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 01:35:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:35:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:35:16: 11000000 INFO @ Tue, 30 Jun 2020 01:35:20: 6000000 INFO @ Tue, 30 Jun 2020 01:35:20: 1000000 INFO @ Tue, 30 Jun 2020 01:35:22: 12000000 INFO @ Tue, 30 Jun 2020 01:35:26: 7000000 INFO @ Tue, 30 Jun 2020 01:35:27: 2000000 INFO @ Tue, 30 Jun 2020 01:35:28: 13000000 INFO @ Tue, 30 Jun 2020 01:35:32: 8000000 INFO @ Tue, 30 Jun 2020 01:35:33: 3000000 INFO @ Tue, 30 Jun 2020 01:35:34: 14000000 INFO @ Tue, 30 Jun 2020 01:35:38: 9000000 INFO @ Tue, 30 Jun 2020 01:35:39: 4000000 INFO @ Tue, 30 Jun 2020 01:35:40: 15000000 INFO @ Tue, 30 Jun 2020 01:35:44: 10000000 INFO @ Tue, 30 Jun 2020 01:35:45: 5000000 INFO @ Tue, 30 Jun 2020 01:35:46: 16000000 INFO @ Tue, 30 Jun 2020 01:35:50: 11000000 INFO @ Tue, 30 Jun 2020 01:35:51: 6000000 INFO @ Tue, 30 Jun 2020 01:35:52: 17000000 INFO @ Tue, 30 Jun 2020 01:35:56: 12000000 INFO @ Tue, 30 Jun 2020 01:35:57: 7000000 INFO @ Tue, 30 Jun 2020 01:35:59: 18000000 INFO @ Tue, 30 Jun 2020 01:36:02: 13000000 INFO @ Tue, 30 Jun 2020 01:36:03: 8000000 INFO @ Tue, 30 Jun 2020 01:36:05: 19000000 INFO @ Tue, 30 Jun 2020 01:36:08: 14000000 INFO @ Tue, 30 Jun 2020 01:36:09: 9000000 INFO @ Tue, 30 Jun 2020 01:36:11: 20000000 INFO @ Tue, 30 Jun 2020 01:36:14: 15000000 INFO @ Tue, 30 Jun 2020 01:36:15: 10000000 INFO @ Tue, 30 Jun 2020 01:36:17: 21000000 INFO @ Tue, 30 Jun 2020 01:36:20: 16000000 INFO @ Tue, 30 Jun 2020 01:36:21: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:36:21: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:36:21: #1 total tags in treatment: 21485351 INFO @ Tue, 30 Jun 2020 01:36:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:36:21: #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 01:36:21: 11000000 INFO @ Tue, 30 Jun 2020 01:36:22: #1 tags after filtering in treatment: 21485351 INFO @ Tue, 30 Jun 2020 01:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:36:22: #1 finished! INFO @ Tue, 30 Jun 2020 01:36:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:36:23: #2 number of paired peaks: 211 WARNING @ Tue, 30 Jun 2020 01:36:23: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 30 Jun 2020 01:36:23: start model_add_line... INFO @ Tue, 30 Jun 2020 01:36:23: start X-correlation... INFO @ Tue, 30 Jun 2020 01:36:23: end of X-cor INFO @ Tue, 30 Jun 2020 01:36:23: #2 finished! INFO @ Tue, 30 Jun 2020 01:36:23: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 01:36:23: #2 alternative fragment length(s) may be 3,37,538,573,598 bps INFO @ Tue, 30 Jun 2020 01:36:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.05_model.r WARNING @ Tue, 30 Jun 2020 01:36:23: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:36:23: #2 You may need to consider one of the other alternative d(s): 3,37,538,573,598 WARNING @ Tue, 30 Jun 2020 01:36:23: #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 01:36:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:36:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:36:26: 17000000 INFO @ Tue, 30 Jun 2020 01:36:27: 12000000 INFO @ Tue, 30 Jun 2020 01:36:32: 13000000 INFO @ Tue, 30 Jun 2020 01:36:32: 18000000 INFO @ Tue, 30 Jun 2020 01:36:38: 14000000 INFO @ Tue, 30 Jun 2020 01:36:38: 19000000 INFO @ Tue, 30 Jun 2020 01:36:43: 15000000 INFO @ Tue, 30 Jun 2020 01:36:44: 20000000 INFO @ Tue, 30 Jun 2020 01:36:49: 16000000 INFO @ Tue, 30 Jun 2020 01:36:50: 21000000 INFO @ Tue, 30 Jun 2020 01:36:53: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:36:53: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:36:53: #1 total tags in treatment: 21485351 INFO @ Tue, 30 Jun 2020 01:36:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:36:53: #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 01:36:54: #1 tags after filtering in treatment: 21485351 INFO @ Tue, 30 Jun 2020 01:36:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:36:54: #1 finished! INFO @ Tue, 30 Jun 2020 01:36:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:36:54: 17000000 INFO @ Tue, 30 Jun 2020 01:36:55: #2 number of paired peaks: 211 WARNING @ Tue, 30 Jun 2020 01:36:55: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 30 Jun 2020 01:36:55: start model_add_line... INFO @ Tue, 30 Jun 2020 01:36:55: start X-correlation... INFO @ Tue, 30 Jun 2020 01:36:55: end of X-cor INFO @ Tue, 30 Jun 2020 01:36:55: #2 finished! INFO @ Tue, 30 Jun 2020 01:36:55: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 01:36:55: #2 alternative fragment length(s) may be 3,37,538,573,598 bps INFO @ Tue, 30 Jun 2020 01:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.10_model.r WARNING @ Tue, 30 Jun 2020 01:36:55: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:36:55: #2 You may need to consider one of the other alternative d(s): 3,37,538,573,598 WARNING @ Tue, 30 Jun 2020 01:36:55: #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 01:36:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:36:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:36:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:37:00: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:37:05: 19000000 INFO @ Tue, 30 Jun 2020 01:37:11: 20000000 INFO @ Tue, 30 Jun 2020 01:37:16: 21000000 INFO @ Tue, 30 Jun 2020 01:37:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:37:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:37:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.05_summits.bed INFO @ Tue, 30 Jun 2020 01:37:17: Done! pass1 - making usageList (470 chroms): 2 millis pass2 - checking and writing primary data (2262 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:37:19: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:37:19: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:37:19: #1 total tags in treatment: 21485351 INFO @ Tue, 30 Jun 2020 01:37:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:37:19: #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 01:37:20: #1 tags after filtering in treatment: 21485351 INFO @ Tue, 30 Jun 2020 01:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:37:20: #1 finished! INFO @ Tue, 30 Jun 2020 01:37:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:37:22: #2 number of paired peaks: 211 WARNING @ Tue, 30 Jun 2020 01:37:22: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 30 Jun 2020 01:37:22: start model_add_line... INFO @ Tue, 30 Jun 2020 01:37:22: start X-correlation... INFO @ Tue, 30 Jun 2020 01:37:22: end of X-cor INFO @ Tue, 30 Jun 2020 01:37:22: #2 finished! INFO @ Tue, 30 Jun 2020 01:37:22: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 01:37:22: #2 alternative fragment length(s) may be 3,37,538,573,598 bps INFO @ Tue, 30 Jun 2020 01:37:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.20_model.r WARNING @ Tue, 30 Jun 2020 01:37:22: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:37:22: #2 You may need to consider one of the other alternative d(s): 3,37,538,573,598 WARNING @ Tue, 30 Jun 2020 01:37:22: #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 01:37:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:37:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.10_summits.bed INFO @ Tue, 30 Jun 2020 01:37:49: Done! pass1 - making usageList (401 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:37:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041399/SRX041399.20_summits.bed INFO @ Tue, 30 Jun 2020 01:38:15: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 9 millis CompletedMACS2peakCalling