Job ID = 6529570 SRX = SRX318810 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: 00:12:53 52337402 reads; of these: 52337402 (100.00%) were unpaired; of these: 1652527 (3.16%) aligned 0 times 38510886 (73.58%) aligned exactly 1 time 12173989 (23.26%) aligned >1 times 96.84% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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 24 files... [bam_rmdupse_core] 17146170 / 50684875 = 0.3383 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 02:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.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 02:51:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:49: 1000000 INFO @ Tue, 30 Jun 2020 02:51:54: 2000000 INFO @ Tue, 30 Jun 2020 02:51:58: 3000000 INFO @ Tue, 30 Jun 2020 02:52:03: 4000000 INFO @ Tue, 30 Jun 2020 02:52:08: 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 02:52:13: 6000000 INFO @ Tue, 30 Jun 2020 02:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.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 02:52:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:17: 7000000 INFO @ Tue, 30 Jun 2020 02:52:19: 1000000 INFO @ Tue, 30 Jun 2020 02:52:22: 8000000 INFO @ Tue, 30 Jun 2020 02:52:24: 2000000 INFO @ Tue, 30 Jun 2020 02:52:27: 9000000 INFO @ Tue, 30 Jun 2020 02:52:29: 3000000 INFO @ Tue, 30 Jun 2020 02:52:32: 10000000 INFO @ Tue, 30 Jun 2020 02:52:33: 4000000 INFO @ Tue, 30 Jun 2020 02:52:36: 11000000 INFO @ Tue, 30 Jun 2020 02:52:38: 5000000 INFO @ Tue, 30 Jun 2020 02:52:41: 12000000 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 02:52:43: 6000000 INFO @ Tue, 30 Jun 2020 02:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.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 02:52:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:46: 13000000 INFO @ Tue, 30 Jun 2020 02:52:48: 7000000 INFO @ Tue, 30 Jun 2020 02:52:49: 1000000 INFO @ Tue, 30 Jun 2020 02:52:51: 14000000 INFO @ Tue, 30 Jun 2020 02:52:53: 8000000 INFO @ Tue, 30 Jun 2020 02:52:54: 2000000 INFO @ Tue, 30 Jun 2020 02:52:56: 15000000 INFO @ Tue, 30 Jun 2020 02:52:58: 9000000 INFO @ Tue, 30 Jun 2020 02:52:59: 3000000 INFO @ Tue, 30 Jun 2020 02:53:01: 16000000 INFO @ Tue, 30 Jun 2020 02:53:02: 10000000 INFO @ Tue, 30 Jun 2020 02:53:04: 4000000 INFO @ Tue, 30 Jun 2020 02:53:06: 17000000 INFO @ Tue, 30 Jun 2020 02:53:07: 11000000 INFO @ Tue, 30 Jun 2020 02:53:09: 5000000 INFO @ Tue, 30 Jun 2020 02:53:11: 18000000 INFO @ Tue, 30 Jun 2020 02:53:12: 12000000 INFO @ Tue, 30 Jun 2020 02:53:14: 6000000 INFO @ Tue, 30 Jun 2020 02:53:16: 19000000 INFO @ Tue, 30 Jun 2020 02:53:17: 13000000 INFO @ Tue, 30 Jun 2020 02:53:18: 7000000 INFO @ Tue, 30 Jun 2020 02:53:20: 20000000 INFO @ Tue, 30 Jun 2020 02:53:22: 14000000 INFO @ Tue, 30 Jun 2020 02:53:23: 8000000 INFO @ Tue, 30 Jun 2020 02:53:25: 21000000 INFO @ Tue, 30 Jun 2020 02:53:27: 15000000 INFO @ Tue, 30 Jun 2020 02:53:28: 9000000 INFO @ Tue, 30 Jun 2020 02:53:30: 22000000 INFO @ Tue, 30 Jun 2020 02:53:32: 16000000 INFO @ Tue, 30 Jun 2020 02:53:33: 10000000 INFO @ Tue, 30 Jun 2020 02:53:35: 23000000 INFO @ Tue, 30 Jun 2020 02:53:37: 17000000 INFO @ Tue, 30 Jun 2020 02:53:38: 11000000 INFO @ Tue, 30 Jun 2020 02:53:40: 24000000 INFO @ Tue, 30 Jun 2020 02:53:41: 18000000 INFO @ Tue, 30 Jun 2020 02:53:43: 12000000 INFO @ Tue, 30 Jun 2020 02:53:45: 25000000 INFO @ Tue, 30 Jun 2020 02:53:46: 19000000 INFO @ Tue, 30 Jun 2020 02:53:47: 13000000 INFO @ Tue, 30 Jun 2020 02:53:50: 26000000 INFO @ Tue, 30 Jun 2020 02:53:51: 20000000 INFO @ Tue, 30 Jun 2020 02:53:52: 14000000 INFO @ Tue, 30 Jun 2020 02:53:55: 27000000 INFO @ Tue, 30 Jun 2020 02:53:56: 21000000 INFO @ Tue, 30 Jun 2020 02:53:57: 15000000 INFO @ Tue, 30 Jun 2020 02:54:00: 28000000 INFO @ Tue, 30 Jun 2020 02:54:01: 22000000 INFO @ Tue, 30 Jun 2020 02:54:02: 16000000 INFO @ Tue, 30 Jun 2020 02:54:05: 29000000 INFO @ Tue, 30 Jun 2020 02:54:06: 23000000 INFO @ Tue, 30 Jun 2020 02:54:07: 17000000 INFO @ Tue, 30 Jun 2020 02:54:09: 30000000 INFO @ Tue, 30 Jun 2020 02:54:11: 24000000 INFO @ Tue, 30 Jun 2020 02:54:12: 18000000 INFO @ Tue, 30 Jun 2020 02:54:14: 31000000 INFO @ Tue, 30 Jun 2020 02:54:15: 25000000 INFO @ Tue, 30 Jun 2020 02:54:17: 19000000 INFO @ Tue, 30 Jun 2020 02:54:19: 32000000 INFO @ Tue, 30 Jun 2020 02:54:20: 26000000 INFO @ Tue, 30 Jun 2020 02:54:21: 20000000 INFO @ Tue, 30 Jun 2020 02:54:24: 33000000 INFO @ Tue, 30 Jun 2020 02:54:26: 27000000 INFO @ Tue, 30 Jun 2020 02:54:26: 21000000 INFO @ Tue, 30 Jun 2020 02:54:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:27: #1 total tags in treatment: 33538705 INFO @ Tue, 30 Jun 2020 02:54:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:27: #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 02:54:28: #1 tags after filtering in treatment: 33538666 INFO @ Tue, 30 Jun 2020 02:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:30: #2 number of paired peaks: 360 WARNING @ Tue, 30 Jun 2020 02:54:30: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:30: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:54:30: #2 alternative fragment length(s) may be 1,20 bps INFO @ Tue, 30 Jun 2020 02:54:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.05_model.r WARNING @ Tue, 30 Jun 2020 02:54:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:30: #2 You may need to consider one of the other alternative d(s): 1,20 WARNING @ Tue, 30 Jun 2020 02:54:30: #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 02:54:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:30: 28000000 INFO @ Tue, 30 Jun 2020 02:54:31: 22000000 INFO @ Tue, 30 Jun 2020 02:54:35: 29000000 INFO @ Tue, 30 Jun 2020 02:54:36: 23000000 INFO @ Tue, 30 Jun 2020 02:54:40: 30000000 INFO @ Tue, 30 Jun 2020 02:54:41: 24000000 INFO @ Tue, 30 Jun 2020 02:54:45: 31000000 INFO @ Tue, 30 Jun 2020 02:54:46: 25000000 INFO @ Tue, 30 Jun 2020 02:54:50: 32000000 INFO @ Tue, 30 Jun 2020 02:54:51: 26000000 INFO @ Tue, 30 Jun 2020 02:54:55: 33000000 INFO @ Tue, 30 Jun 2020 02:54:56: 27000000 INFO @ Tue, 30 Jun 2020 02:54:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:58: #1 total tags in treatment: 33538705 INFO @ Tue, 30 Jun 2020 02:54:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:58: #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 02:54:58: #1 tags after filtering in treatment: 33538666 INFO @ Tue, 30 Jun 2020 02:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:00: 28000000 INFO @ Tue, 30 Jun 2020 02:55:01: #2 number of paired peaks: 360 WARNING @ Tue, 30 Jun 2020 02:55:01: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:01: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:01: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:01: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:01: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:01: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:55:01: #2 alternative fragment length(s) may be 1,20 bps INFO @ Tue, 30 Jun 2020 02:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.10_model.r WARNING @ Tue, 30 Jun 2020 02:55:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:01: #2 You may need to consider one of the other alternative d(s): 1,20 WARNING @ Tue, 30 Jun 2020 02:55:01: #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 02:55:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:55:05: 29000000 INFO @ Tue, 30 Jun 2020 02:55:10: 30000000 INFO @ Tue, 30 Jun 2020 02:55:15: 31000000 INFO @ Tue, 30 Jun 2020 02:55:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:20: 32000000 INFO @ Tue, 30 Jun 2020 02:55:24: 33000000 INFO @ Tue, 30 Jun 2020 02:55:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:55:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:55:27: #1 total tags in treatment: 33538705 INFO @ Tue, 30 Jun 2020 02:55:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:27: #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 02:55:28: #1 tags after filtering in treatment: 33538666 INFO @ Tue, 30 Jun 2020 02:55:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:30: #2 number of paired peaks: 360 WARNING @ Tue, 30 Jun 2020 02:55:30: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:30: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:55:30: #2 alternative fragment length(s) may be 1,20 bps INFO @ Tue, 30 Jun 2020 02:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.20_model.r WARNING @ Tue, 30 Jun 2020 02:55:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:30: #2 You may need to consider one of the other alternative d(s): 1,20 WARNING @ Tue, 30 Jun 2020 02:55:30: #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 02:55:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.05_summits.bed INFO @ Tue, 30 Jun 2020 02:55:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.10_summits.bed INFO @ Tue, 30 Jun 2020 02:56:10: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:56:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318810/SRX318810.20_summits.bed INFO @ Tue, 30 Jun 2020 02:56:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling