Job ID = 6458740 SRX = SRX5431043 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:12:34 prefetch.2.10.7: 1) Downloading 'SRR8632342'... 2020-06-21T13:12:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:16:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:16:13 prefetch.2.10.7: 1) 'SRR8632342' was downloaded successfully Read 29516345 spots for SRR8632342/SRR8632342.sra Written 29516345 spots for SRR8632342/SRR8632342.sra 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: 00:09:01 29516345 reads; of these: 29516345 (100.00%) were unpaired; of these: 2099492 (7.11%) aligned 0 times 19060039 (64.57%) aligned exactly 1 time 8356814 (28.31%) aligned >1 times 92.89% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 4876569 / 27416853 = 0.1779 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 @ Sun, 21 Jun 2020 22:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.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 @ Sun, 21 Jun 2020 22:34:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:30: 1000000 INFO @ Sun, 21 Jun 2020 22:34:37: 2000000 INFO @ Sun, 21 Jun 2020 22:34:44: 3000000 INFO @ Sun, 21 Jun 2020 22:34:50: 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 @ Sun, 21 Jun 2020 22:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.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 @ Sun, 21 Jun 2020 22:34:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:57: 5000000 INFO @ Sun, 21 Jun 2020 22:34:58: 1000000 INFO @ Sun, 21 Jun 2020 22:35:04: 2000000 INFO @ Sun, 21 Jun 2020 22:35:04: 6000000 INFO @ Sun, 21 Jun 2020 22:35:09: 3000000 INFO @ Sun, 21 Jun 2020 22:35:11: 7000000 INFO @ Sun, 21 Jun 2020 22:35:14: 4000000 INFO @ Sun, 21 Jun 2020 22:35:18: 8000000 INFO @ Sun, 21 Jun 2020 22:35:19: 5000000 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 @ Sun, 21 Jun 2020 22:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.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 @ Sun, 21 Jun 2020 22:35:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:35:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:35:25: 6000000 INFO @ Sun, 21 Jun 2020 22:35:25: 9000000 INFO @ Sun, 21 Jun 2020 22:35:30: 7000000 INFO @ Sun, 21 Jun 2020 22:35:30: 1000000 INFO @ Sun, 21 Jun 2020 22:35:32: 10000000 INFO @ Sun, 21 Jun 2020 22:35:35: 8000000 INFO @ Sun, 21 Jun 2020 22:35:37: 2000000 INFO @ Sun, 21 Jun 2020 22:35:39: 11000000 INFO @ Sun, 21 Jun 2020 22:35:41: 9000000 INFO @ Sun, 21 Jun 2020 22:35:44: 3000000 INFO @ Sun, 21 Jun 2020 22:35:46: 12000000 INFO @ Sun, 21 Jun 2020 22:35:46: 10000000 INFO @ Sun, 21 Jun 2020 22:35:51: 4000000 INFO @ Sun, 21 Jun 2020 22:35:51: 11000000 INFO @ Sun, 21 Jun 2020 22:35:53: 13000000 INFO @ Sun, 21 Jun 2020 22:35:56: 12000000 INFO @ Sun, 21 Jun 2020 22:35:58: 5000000 INFO @ Sun, 21 Jun 2020 22:35:59: 14000000 INFO @ Sun, 21 Jun 2020 22:36:01: 13000000 INFO @ Sun, 21 Jun 2020 22:36:05: 6000000 INFO @ Sun, 21 Jun 2020 22:36:06: 15000000 INFO @ Sun, 21 Jun 2020 22:36:07: 14000000 INFO @ Sun, 21 Jun 2020 22:36:12: 7000000 INFO @ Sun, 21 Jun 2020 22:36:12: 15000000 INFO @ Sun, 21 Jun 2020 22:36:13: 16000000 INFO @ Sun, 21 Jun 2020 22:36:17: 16000000 INFO @ Sun, 21 Jun 2020 22:36:19: 8000000 INFO @ Sun, 21 Jun 2020 22:36:20: 17000000 INFO @ Sun, 21 Jun 2020 22:36:22: 17000000 INFO @ Sun, 21 Jun 2020 22:36:26: 9000000 INFO @ Sun, 21 Jun 2020 22:36:27: 18000000 INFO @ Sun, 21 Jun 2020 22:36:28: 18000000 INFO @ Sun, 21 Jun 2020 22:36:33: 10000000 INFO @ Sun, 21 Jun 2020 22:36:34: 19000000 INFO @ Sun, 21 Jun 2020 22:36:35: 19000000 INFO @ Sun, 21 Jun 2020 22:36:40: 11000000 INFO @ Sun, 21 Jun 2020 22:36:40: 20000000 INFO @ Sun, 21 Jun 2020 22:36:42: 20000000 INFO @ Sun, 21 Jun 2020 22:36:45: 21000000 INFO @ Sun, 21 Jun 2020 22:36:47: 12000000 INFO @ Sun, 21 Jun 2020 22:36:49: 21000000 INFO @ Sun, 21 Jun 2020 22:36:51: 22000000 INFO @ Sun, 21 Jun 2020 22:36:54: 13000000 INFO @ Sun, 21 Jun 2020 22:36:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:36:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:36:54: #1 total tags in treatment: 22540284 INFO @ Sun, 21 Jun 2020 22:36:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:36:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:36:55: #1 tags after filtering in treatment: 22540284 INFO @ Sun, 21 Jun 2020 22:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:36:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:36:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:36:56: 22000000 INFO @ Sun, 21 Jun 2020 22:36:57: #2 number of paired peaks: 600 WARNING @ Sun, 21 Jun 2020 22:36:57: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Sun, 21 Jun 2020 22:36:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:36:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:36:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:36:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:36:57: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:36:57: #2 alternative fragment length(s) may be 1,14 bps INFO @ Sun, 21 Jun 2020 22:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.10_model.r WARNING @ Sun, 21 Jun 2020 22:36:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:36:57: #2 You may need to consider one of the other alternative d(s): 1,14 WARNING @ Sun, 21 Jun 2020 22:36:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:36:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:37:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:37:00: #1 total tags in treatment: 22540284 INFO @ Sun, 21 Jun 2020 22:37:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:37:00: 14000000 INFO @ Sun, 21 Jun 2020 22:37:01: #1 tags after filtering in treatment: 22540284 INFO @ Sun, 21 Jun 2020 22:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:02: #2 number of paired peaks: 600 WARNING @ Sun, 21 Jun 2020 22:37:02: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Sun, 21 Jun 2020 22:37:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:03: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:37:03: #2 alternative fragment length(s) may be 1,14 bps INFO @ Sun, 21 Jun 2020 22:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.05_model.r WARNING @ Sun, 21 Jun 2020 22:37:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:03: #2 You may need to consider one of the other alternative d(s): 1,14 WARNING @ Sun, 21 Jun 2020 22:37:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:37:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:07: 15000000 INFO @ Sun, 21 Jun 2020 22:37:14: 16000000 INFO @ Sun, 21 Jun 2020 22:37:21: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:37:28: 18000000 INFO @ Sun, 21 Jun 2020 22:37:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:37:36: 19000000 INFO @ Sun, 21 Jun 2020 22:37:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:37:43: 20000000 INFO @ Sun, 21 Jun 2020 22:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:37:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.10_summits.bed INFO @ Sun, 21 Jun 2020 22:37:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:37:50: 21000000 INFO @ Sun, 21 Jun 2020 22:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.05_summits.bed INFO @ Sun, 21 Jun 2020 22:37:53: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:37:57: 22000000 INFO @ Sun, 21 Jun 2020 22:38:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:38:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:38:01: #1 total tags in treatment: 22540284 INFO @ Sun, 21 Jun 2020 22:38:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:38:02: #1 tags after filtering in treatment: 22540284 INFO @ Sun, 21 Jun 2020 22:38:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:04: #2 number of paired peaks: 600 WARNING @ Sun, 21 Jun 2020 22:38:04: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Sun, 21 Jun 2020 22:38:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:04: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:38:04: #2 alternative fragment length(s) may be 1,14 bps INFO @ Sun, 21 Jun 2020 22:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.20_model.r WARNING @ Sun, 21 Jun 2020 22:38:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:04: #2 You may need to consider one of the other alternative d(s): 1,14 WARNING @ Sun, 21 Jun 2020 22:38:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:38:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:38:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431043/SRX5431043.20_summits.bed INFO @ Sun, 21 Jun 2020 22:38:55: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling