Job ID = 6529737 SRX = SRX4664656 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: 00:10:20 31909608 reads; of these: 31909608 (100.00%) were unpaired; of these: 938005 (2.94%) aligned 0 times 20960245 (65.69%) aligned exactly 1 time 10011358 (31.37%) aligned >1 times 97.06% overall alignment rate Time searching: 00:10:20 Overall time: 00:10:20 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] 5513018 / 30971603 = 0.1780 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 02:47:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.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 02:47:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:29: 1000000 INFO @ Tue, 30 Jun 2020 02:47:35: 2000000 INFO @ Tue, 30 Jun 2020 02:47:41: 3000000 INFO @ Tue, 30 Jun 2020 02:47:47: 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 02:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.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 02:47:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:53: 5000000 INFO @ Tue, 30 Jun 2020 02:48:00: 6000000 INFO @ Tue, 30 Jun 2020 02:48:00: 1000000 INFO @ Tue, 30 Jun 2020 02:48:07: 7000000 INFO @ Tue, 30 Jun 2020 02:48:08: 2000000 INFO @ Tue, 30 Jun 2020 02:48:14: 8000000 INFO @ Tue, 30 Jun 2020 02:48:15: 3000000 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 02:48:21: 9000000 INFO @ Tue, 30 Jun 2020 02:48:23: 4000000 INFO @ Tue, 30 Jun 2020 02:48:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.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 02:48:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:29: 10000000 INFO @ Tue, 30 Jun 2020 02:48:30: 5000000 INFO @ Tue, 30 Jun 2020 02:48:30: 1000000 INFO @ Tue, 30 Jun 2020 02:48:36: 11000000 INFO @ Tue, 30 Jun 2020 02:48:38: 6000000 INFO @ Tue, 30 Jun 2020 02:48:38: 2000000 INFO @ Tue, 30 Jun 2020 02:48:44: 12000000 INFO @ Tue, 30 Jun 2020 02:48:45: 7000000 INFO @ Tue, 30 Jun 2020 02:48:45: 3000000 INFO @ Tue, 30 Jun 2020 02:48:51: 13000000 INFO @ Tue, 30 Jun 2020 02:48:52: 8000000 INFO @ Tue, 30 Jun 2020 02:48:53: 4000000 INFO @ Tue, 30 Jun 2020 02:48:58: 14000000 INFO @ Tue, 30 Jun 2020 02:49:00: 5000000 INFO @ Tue, 30 Jun 2020 02:49:00: 9000000 INFO @ Tue, 30 Jun 2020 02:49:06: 15000000 INFO @ Tue, 30 Jun 2020 02:49:07: 6000000 INFO @ Tue, 30 Jun 2020 02:49:08: 10000000 INFO @ Tue, 30 Jun 2020 02:49:13: 16000000 INFO @ Tue, 30 Jun 2020 02:49:14: 7000000 INFO @ Tue, 30 Jun 2020 02:49:15: 11000000 INFO @ Tue, 30 Jun 2020 02:49:20: 17000000 INFO @ Tue, 30 Jun 2020 02:49:22: 8000000 INFO @ Tue, 30 Jun 2020 02:49:23: 12000000 INFO @ Tue, 30 Jun 2020 02:49:28: 18000000 INFO @ Tue, 30 Jun 2020 02:49:29: 9000000 INFO @ Tue, 30 Jun 2020 02:49:30: 13000000 INFO @ Tue, 30 Jun 2020 02:49:36: 19000000 INFO @ Tue, 30 Jun 2020 02:49:37: 10000000 INFO @ Tue, 30 Jun 2020 02:49:38: 14000000 INFO @ Tue, 30 Jun 2020 02:49:43: 20000000 INFO @ Tue, 30 Jun 2020 02:49:44: 11000000 INFO @ Tue, 30 Jun 2020 02:49:46: 15000000 INFO @ Tue, 30 Jun 2020 02:49:51: 21000000 INFO @ Tue, 30 Jun 2020 02:49:51: 12000000 INFO @ Tue, 30 Jun 2020 02:49:53: 16000000 INFO @ Tue, 30 Jun 2020 02:49:58: 13000000 INFO @ Tue, 30 Jun 2020 02:49:59: 22000000 INFO @ Tue, 30 Jun 2020 02:50:01: 17000000 INFO @ Tue, 30 Jun 2020 02:50:05: 14000000 INFO @ Tue, 30 Jun 2020 02:50:06: 23000000 INFO @ Tue, 30 Jun 2020 02:50:08: 18000000 INFO @ Tue, 30 Jun 2020 02:50:13: 15000000 INFO @ Tue, 30 Jun 2020 02:50:14: 24000000 INFO @ Tue, 30 Jun 2020 02:50:16: 19000000 INFO @ Tue, 30 Jun 2020 02:50:20: 16000000 INFO @ Tue, 30 Jun 2020 02:50:21: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:50:24: 20000000 INFO @ Tue, 30 Jun 2020 02:50:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:25: #1 total tags in treatment: 25458585 INFO @ Tue, 30 Jun 2020 02:50:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:25: #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 02:50:26: #1 tags after filtering in treatment: 25458532 INFO @ Tue, 30 Jun 2020 02:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:27: 17000000 INFO @ Tue, 30 Jun 2020 02:50:27: #2 number of paired peaks: 820 WARNING @ Tue, 30 Jun 2020 02:50:27: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:28: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:50:28: #2 alternative fragment length(s) may be 1,49 bps INFO @ Tue, 30 Jun 2020 02:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.05_model.r WARNING @ Tue, 30 Jun 2020 02:50:28: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:28: #2 You may need to consider one of the other alternative d(s): 1,49 WARNING @ Tue, 30 Jun 2020 02:50:28: #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 02:50:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:31: 21000000 INFO @ Tue, 30 Jun 2020 02:50:35: 18000000 INFO @ Tue, 30 Jun 2020 02:50:39: 22000000 INFO @ Tue, 30 Jun 2020 02:50:42: 19000000 INFO @ Tue, 30 Jun 2020 02:50:47: 23000000 INFO @ Tue, 30 Jun 2020 02:50:49: 20000000 INFO @ Tue, 30 Jun 2020 02:50:54: 24000000 INFO @ Tue, 30 Jun 2020 02:50:56: 21000000 INFO @ Tue, 30 Jun 2020 02:51:02: 25000000 INFO @ Tue, 30 Jun 2020 02:51:03: 22000000 INFO @ Tue, 30 Jun 2020 02:51:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:51:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:51:05: #1 total tags in treatment: 25458585 INFO @ Tue, 30 Jun 2020 02:51:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:05: #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 02:51:06: #1 tags after filtering in treatment: 25458532 INFO @ Tue, 30 Jun 2020 02:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:08: #2 number of paired peaks: 820 WARNING @ Tue, 30 Jun 2020 02:51:08: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:08: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:51:08: #2 alternative fragment length(s) may be 1,49 bps INFO @ Tue, 30 Jun 2020 02:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.10_model.r WARNING @ Tue, 30 Jun 2020 02:51:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:08: #2 You may need to consider one of the other alternative d(s): 1,49 WARNING @ Tue, 30 Jun 2020 02:51:08: #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 02:51:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:10: 23000000 INFO @ Tue, 30 Jun 2020 02:51:16: 24000000 INFO @ Tue, 30 Jun 2020 02:51:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:23: 25000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:51:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:51:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:51:26: #1 total tags in treatment: 25458585 INFO @ Tue, 30 Jun 2020 02:51:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:26: #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 02:51:26: #1 tags after filtering in treatment: 25458532 INFO @ Tue, 30 Jun 2020 02:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:28: #2 number of paired peaks: 820 WARNING @ Tue, 30 Jun 2020 02:51:28: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:29: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:51:29: #2 alternative fragment length(s) may be 1,49 bps INFO @ Tue, 30 Jun 2020 02:51:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.20_model.r WARNING @ Tue, 30 Jun 2020 02:51:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:29: #2 You may need to consider one of the other alternative d(s): 1,49 WARNING @ Tue, 30 Jun 2020 02:51:29: #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 02:51:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.05_summits.bed INFO @ Tue, 30 Jun 2020 02:51:42: Done! pass1 - making usageList (609 chroms): 1 millis pass2 - checking and writing primary data (3711 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.10_summits.bed INFO @ Tue, 30 Jun 2020 02:52:19: Done! pass1 - making usageList (526 chroms): 1 millis pass2 - checking and writing primary data (2316 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:52:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664656/SRX4664656.20_summits.bed INFO @ Tue, 30 Jun 2020 02:52:39: Done! pass1 - making usageList (375 chroms): 2 millis pass2 - checking and writing primary data (947 records, 4 fields): 12 millis CompletedMACS2peakCalling