Job ID = 6457996 SRX = SRX4933899 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:09:24 prefetch.2.10.7: 1) Downloading 'SRR8107290'... 2020-06-21T12:09:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:26:33 prefetch.2.10.7: HTTPS download failed 2020-06-21T12:26:33 prefetch.2.10.7: 1) failed to download SRR8107290 2020-06-21T12:26:47 prefetch.2.10.7: 1) Downloading 'SRR8107290'... 2020-06-21T12:26:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:26:47 prefetch.2.10.7: Continue download of 'SRR8107290' from 1335605776 2020-06-21T12:26:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:26:55 prefetch.2.10.7: 1) 'SRR8107290' was downloaded successfully Read 38659503 spots for SRR8107290/SRR8107290.sra Written 38659503 spots for SRR8107290/SRR8107290.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: 00:12:06 38659503 reads; of these: 38659503 (100.00%) were unpaired; of these: 1229457 (3.18%) aligned 0 times 26844535 (69.44%) aligned exactly 1 time 10585511 (27.38%) aligned >1 times 96.82% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 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] 7218598 / 37430046 = 0.1929 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 21:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.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 21:51:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:51: 1000000 INFO @ Sun, 21 Jun 2020 21:51:56: 2000000 INFO @ Sun, 21 Jun 2020 21:52:02: 3000000 INFO @ Sun, 21 Jun 2020 21:52:08: 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 21:52:14: 5000000 INFO @ Sun, 21 Jun 2020 21:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.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 21:52:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:20: 6000000 INFO @ Sun, 21 Jun 2020 21:52:23: 1000000 INFO @ Sun, 21 Jun 2020 21:52:27: 7000000 INFO @ Sun, 21 Jun 2020 21:52:31: 2000000 INFO @ Sun, 21 Jun 2020 21:52:34: 8000000 INFO @ Sun, 21 Jun 2020 21:52:38: 3000000 INFO @ Sun, 21 Jun 2020 21:52:41: 9000000 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 21:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.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 21:52:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:46: 4000000 INFO @ Sun, 21 Jun 2020 21:52:48: 10000000 INFO @ Sun, 21 Jun 2020 21:52:52: 1000000 INFO @ Sun, 21 Jun 2020 21:52:54: 5000000 INFO @ Sun, 21 Jun 2020 21:52:55: 11000000 INFO @ Sun, 21 Jun 2020 21:52:59: 2000000 INFO @ Sun, 21 Jun 2020 21:53:02: 6000000 INFO @ Sun, 21 Jun 2020 21:53:03: 12000000 INFO @ Sun, 21 Jun 2020 21:53:07: 3000000 INFO @ Sun, 21 Jun 2020 21:53:09: 7000000 INFO @ Sun, 21 Jun 2020 21:53:10: 13000000 INFO @ Sun, 21 Jun 2020 21:53:14: 4000000 INFO @ Sun, 21 Jun 2020 21:53:17: 14000000 INFO @ Sun, 21 Jun 2020 21:53:17: 8000000 INFO @ Sun, 21 Jun 2020 21:53:21: 5000000 INFO @ Sun, 21 Jun 2020 21:53:24: 15000000 INFO @ Sun, 21 Jun 2020 21:53:26: 9000000 INFO @ Sun, 21 Jun 2020 21:53:28: 6000000 INFO @ Sun, 21 Jun 2020 21:53:31: 16000000 INFO @ Sun, 21 Jun 2020 21:53:33: 10000000 INFO @ Sun, 21 Jun 2020 21:53:35: 7000000 INFO @ Sun, 21 Jun 2020 21:53:39: 17000000 INFO @ Sun, 21 Jun 2020 21:53:41: 11000000 INFO @ Sun, 21 Jun 2020 21:53:43: 8000000 INFO @ Sun, 21 Jun 2020 21:53:46: 18000000 INFO @ Sun, 21 Jun 2020 21:53:48: 12000000 INFO @ Sun, 21 Jun 2020 21:53:50: 9000000 INFO @ Sun, 21 Jun 2020 21:53:54: 19000000 INFO @ Sun, 21 Jun 2020 21:53:56: 13000000 INFO @ Sun, 21 Jun 2020 21:53:58: 10000000 INFO @ Sun, 21 Jun 2020 21:54:01: 20000000 INFO @ Sun, 21 Jun 2020 21:54:04: 14000000 INFO @ Sun, 21 Jun 2020 21:54:06: 11000000 INFO @ Sun, 21 Jun 2020 21:54:09: 21000000 INFO @ Sun, 21 Jun 2020 21:54:11: 15000000 INFO @ Sun, 21 Jun 2020 21:54:13: 12000000 INFO @ Sun, 21 Jun 2020 21:54:16: 22000000 INFO @ Sun, 21 Jun 2020 21:54:19: 16000000 INFO @ Sun, 21 Jun 2020 21:54:20: 13000000 INFO @ Sun, 21 Jun 2020 21:54:24: 23000000 INFO @ Sun, 21 Jun 2020 21:54:27: 17000000 INFO @ Sun, 21 Jun 2020 21:54:28: 14000000 INFO @ Sun, 21 Jun 2020 21:54:31: 24000000 INFO @ Sun, 21 Jun 2020 21:54:35: 18000000 INFO @ Sun, 21 Jun 2020 21:54:35: 15000000 INFO @ Sun, 21 Jun 2020 21:54:39: 25000000 INFO @ Sun, 21 Jun 2020 21:54:42: 19000000 INFO @ Sun, 21 Jun 2020 21:54:43: 16000000 INFO @ Sun, 21 Jun 2020 21:54:47: 26000000 INFO @ Sun, 21 Jun 2020 21:54:50: 20000000 INFO @ Sun, 21 Jun 2020 21:54:51: 17000000 INFO @ Sun, 21 Jun 2020 21:54:55: 27000000 INFO @ Sun, 21 Jun 2020 21:54:58: 21000000 INFO @ Sun, 21 Jun 2020 21:54:59: 18000000 INFO @ Sun, 21 Jun 2020 21:55:02: 28000000 INFO @ Sun, 21 Jun 2020 21:55:06: 19000000 INFO @ Sun, 21 Jun 2020 21:55:06: 22000000 INFO @ Sun, 21 Jun 2020 21:55:10: 29000000 INFO @ Sun, 21 Jun 2020 21:55:14: 20000000 INFO @ Sun, 21 Jun 2020 21:55:15: 23000000 INFO @ Sun, 21 Jun 2020 21:55:18: 30000000 INFO @ Sun, 21 Jun 2020 21:55:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:20: #1 total tags in treatment: 30211448 INFO @ Sun, 21 Jun 2020 21:55:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:20: #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 21:55:21: #1 tags after filtering in treatment: 30211447 INFO @ Sun, 21 Jun 2020 21:55:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:21: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:22: 21000000 INFO @ Sun, 21 Jun 2020 21:55:23: #2 number of paired peaks: 174 WARNING @ Sun, 21 Jun 2020 21:55:23: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:23: 24000000 INFO @ Sun, 21 Jun 2020 21:55:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:23: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:55:23: #2 alternative fragment length(s) may be 2,19,44 bps INFO @ Sun, 21 Jun 2020 21:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.05_model.r WARNING @ Sun, 21 Jun 2020 21:55:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:23: #2 You may need to consider one of the other alternative d(s): 2,19,44 WARNING @ Sun, 21 Jun 2020 21:55:23: #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 21:55:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:29: 22000000 INFO @ Sun, 21 Jun 2020 21:55:31: 25000000 INFO @ Sun, 21 Jun 2020 21:55:36: 23000000 INFO @ Sun, 21 Jun 2020 21:55:40: 26000000 INFO @ Sun, 21 Jun 2020 21:55:44: 24000000 INFO @ Sun, 21 Jun 2020 21:55:48: 27000000 INFO @ Sun, 21 Jun 2020 21:55:52: 25000000 INFO @ Sun, 21 Jun 2020 21:55:56: 28000000 INFO @ Sun, 21 Jun 2020 21:55:59: 26000000 INFO @ Sun, 21 Jun 2020 21:56:04: 29000000 INFO @ Sun, 21 Jun 2020 21:56:07: 27000000 INFO @ Sun, 21 Jun 2020 21:56:13: 30000000 INFO @ Sun, 21 Jun 2020 21:56:14: 28000000 INFO @ Sun, 21 Jun 2020 21:56:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:15: #1 total tags in treatment: 30211448 INFO @ Sun, 21 Jun 2020 21:56:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:15: #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 21:56:16: #1 tags after filtering in treatment: 30211447 INFO @ Sun, 21 Jun 2020 21:56:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:18: #2 number of paired peaks: 174 WARNING @ Sun, 21 Jun 2020 21:56:18: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:18: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:56:18: #2 alternative fragment length(s) may be 2,19,44 bps INFO @ Sun, 21 Jun 2020 21:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.10_model.r WARNING @ Sun, 21 Jun 2020 21:56:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:18: #2 You may need to consider one of the other alternative d(s): 2,19,44 WARNING @ Sun, 21 Jun 2020 21:56:18: #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 21:56:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:21: 29000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:28: 30000000 INFO @ Sun, 21 Jun 2020 21:56:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:30: #1 total tags in treatment: 30211448 INFO @ Sun, 21 Jun 2020 21:56:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:30: #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 21:56:30: #1 tags after filtering in treatment: 30211447 INFO @ Sun, 21 Jun 2020 21:56:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:32: #2 number of paired peaks: 174 WARNING @ Sun, 21 Jun 2020 21:56:32: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:32: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:56:32: #2 alternative fragment length(s) may be 2,19,44 bps INFO @ Sun, 21 Jun 2020 21:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:32: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:32: #2 You may need to consider one of the other alternative d(s): 2,19,44 WARNING @ Sun, 21 Jun 2020 21:56:32: #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 21:56:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.10_summits.bed INFO @ Sun, 21 Jun 2020 21:57:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933899/SRX4933899.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:46: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling