Job ID = 6528400 SRX = SRX5736607 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:53:14 prefetch.2.10.7: 1) Downloading 'SRR8957017'... 2020-06-29T14:53:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:07:26 prefetch.2.10.7: HTTPS download failed 2020-06-29T15:07:26 prefetch.2.10.7: 1) failed to download SRR8957017 2020-06-29T15:07:40 prefetch.2.10.7: 1) Downloading 'SRR8957017'... 2020-06-29T15:07:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:07:40 prefetch.2.10.7: Continue download of 'SRR8957017' from 602189085 2020-06-29T15:07:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:07:48 prefetch.2.10.7: 1) 'SRR8957017' was downloaded successfully Read 25039537 spots for SRR8957017/SRR8957017.sra Written 25039537 spots for SRR8957017/SRR8957017.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: 00:08:10 25039537 reads; of these: 25039537 (100.00%) were unpaired; of these: 582914 (2.33%) aligned 0 times 18306201 (73.11%) aligned exactly 1 time 6150422 (24.56%) aligned >1 times 97.67% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3108810 / 24456623 = 0.1271 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 00:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.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 00:29:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:29:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:29:49: 1000000 INFO @ Tue, 30 Jun 2020 00:29:56: 2000000 INFO @ Tue, 30 Jun 2020 00:30:02: 3000000 INFO @ Tue, 30 Jun 2020 00:30:08: 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 @ Tue, 30 Jun 2020 00:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.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 00:30:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:30:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:30:14: 5000000 INFO @ Tue, 30 Jun 2020 00:30:19: 1000000 INFO @ Tue, 30 Jun 2020 00:30:21: 6000000 INFO @ Tue, 30 Jun 2020 00:30:26: 2000000 INFO @ Tue, 30 Jun 2020 00:30:27: 7000000 INFO @ Tue, 30 Jun 2020 00:30:32: 3000000 INFO @ Tue, 30 Jun 2020 00:30:34: 8000000 INFO @ Tue, 30 Jun 2020 00:30:38: 4000000 INFO @ Tue, 30 Jun 2020 00:30:40: 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 @ Tue, 30 Jun 2020 00:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.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 00:30:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:30:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:30:45: 5000000 INFO @ Tue, 30 Jun 2020 00:30:47: 10000000 INFO @ Tue, 30 Jun 2020 00:30:49: 1000000 INFO @ Tue, 30 Jun 2020 00:30:51: 6000000 INFO @ Tue, 30 Jun 2020 00:30:54: 11000000 INFO @ Tue, 30 Jun 2020 00:30:56: 2000000 INFO @ Tue, 30 Jun 2020 00:30:58: 7000000 INFO @ Tue, 30 Jun 2020 00:31:00: 12000000 INFO @ Tue, 30 Jun 2020 00:31:03: 3000000 INFO @ Tue, 30 Jun 2020 00:31:05: 8000000 INFO @ Tue, 30 Jun 2020 00:31:07: 13000000 INFO @ Tue, 30 Jun 2020 00:31:09: 4000000 INFO @ Tue, 30 Jun 2020 00:31:11: 9000000 INFO @ Tue, 30 Jun 2020 00:31:13: 14000000 INFO @ Tue, 30 Jun 2020 00:31:15: 5000000 INFO @ Tue, 30 Jun 2020 00:31:18: 10000000 INFO @ Tue, 30 Jun 2020 00:31:20: 15000000 INFO @ Tue, 30 Jun 2020 00:31:22: 6000000 INFO @ Tue, 30 Jun 2020 00:31:24: 11000000 INFO @ Tue, 30 Jun 2020 00:31:26: 16000000 INFO @ Tue, 30 Jun 2020 00:31:28: 7000000 INFO @ Tue, 30 Jun 2020 00:31:30: 12000000 INFO @ Tue, 30 Jun 2020 00:31:33: 17000000 INFO @ Tue, 30 Jun 2020 00:31:34: 8000000 INFO @ Tue, 30 Jun 2020 00:31:37: 13000000 INFO @ Tue, 30 Jun 2020 00:31:39: 18000000 INFO @ Tue, 30 Jun 2020 00:31:40: 9000000 INFO @ Tue, 30 Jun 2020 00:31:43: 14000000 INFO @ Tue, 30 Jun 2020 00:31:45: 19000000 INFO @ Tue, 30 Jun 2020 00:31:47: 10000000 INFO @ Tue, 30 Jun 2020 00:31:49: 15000000 INFO @ Tue, 30 Jun 2020 00:31:52: 20000000 INFO @ Tue, 30 Jun 2020 00:31:53: 11000000 INFO @ Tue, 30 Jun 2020 00:31:56: 16000000 INFO @ Tue, 30 Jun 2020 00:31:58: 21000000 INFO @ Tue, 30 Jun 2020 00:31:59: 12000000 INFO @ Tue, 30 Jun 2020 00:32:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:32:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:32:01: #1 total tags in treatment: 21347813 INFO @ Tue, 30 Jun 2020 00:32:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:32:01: #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 00:32:01: #1 tags after filtering in treatment: 21347813 INFO @ Tue, 30 Jun 2020 00:32:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:32:01: #1 finished! INFO @ Tue, 30 Jun 2020 00:32:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:32:02: 17000000 INFO @ Tue, 30 Jun 2020 00:32:03: #2 number of paired peaks: 649 WARNING @ Tue, 30 Jun 2020 00:32:03: Fewer paired peaks (649) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 649 pairs to build model! INFO @ Tue, 30 Jun 2020 00:32:03: start model_add_line... INFO @ Tue, 30 Jun 2020 00:32:03: start X-correlation... INFO @ Tue, 30 Jun 2020 00:32:03: end of X-cor INFO @ Tue, 30 Jun 2020 00:32:03: #2 finished! INFO @ Tue, 30 Jun 2020 00:32:03: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:32:03: #2 alternative fragment length(s) may be 2,18 bps INFO @ Tue, 30 Jun 2020 00:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.05_model.r WARNING @ Tue, 30 Jun 2020 00:32:03: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:32:03: #2 You may need to consider one of the other alternative d(s): 2,18 WARNING @ Tue, 30 Jun 2020 00:32:03: #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 00:32:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:32:06: 13000000 INFO @ Tue, 30 Jun 2020 00:32:08: 18000000 INFO @ Tue, 30 Jun 2020 00:32:12: 14000000 INFO @ Tue, 30 Jun 2020 00:32:14: 19000000 INFO @ Tue, 30 Jun 2020 00:32:18: 15000000 INFO @ Tue, 30 Jun 2020 00:32:21: 20000000 INFO @ Tue, 30 Jun 2020 00:32:24: 16000000 INFO @ Tue, 30 Jun 2020 00:32:27: 21000000 INFO @ Tue, 30 Jun 2020 00:32:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:32:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:32:29: #1 total tags in treatment: 21347813 INFO @ Tue, 30 Jun 2020 00:32:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:32:29: #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 00:32:30: #1 tags after filtering in treatment: 21347813 INFO @ Tue, 30 Jun 2020 00:32:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:32:30: #1 finished! INFO @ Tue, 30 Jun 2020 00:32:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:32:30: 17000000 INFO @ Tue, 30 Jun 2020 00:32:31: #2 number of paired peaks: 649 WARNING @ Tue, 30 Jun 2020 00:32:31: Fewer paired peaks (649) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 649 pairs to build model! INFO @ Tue, 30 Jun 2020 00:32:31: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:32:31: start X-correlation... INFO @ Tue, 30 Jun 2020 00:32:31: end of X-cor INFO @ Tue, 30 Jun 2020 00:32:31: #2 finished! INFO @ Tue, 30 Jun 2020 00:32:31: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:32:31: #2 alternative fragment length(s) may be 2,18 bps INFO @ Tue, 30 Jun 2020 00:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.10_model.r WARNING @ Tue, 30 Jun 2020 00:32:31: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:32:31: #2 You may need to consider one of the other alternative d(s): 2,18 WARNING @ Tue, 30 Jun 2020 00:32:31: #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 00:32:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:32:37: 18000000 INFO @ Tue, 30 Jun 2020 00:32:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:32:43: 19000000 INFO @ Tue, 30 Jun 2020 00:32:49: 20000000 INFO @ Tue, 30 Jun 2020 00:32:55: 21000000 INFO @ Tue, 30 Jun 2020 00:32:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:32:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:32:57: #1 total tags in treatment: 21347813 INFO @ Tue, 30 Jun 2020 00:32:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:32:57: #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 00:32:57: #1 tags after filtering in treatment: 21347813 INFO @ Tue, 30 Jun 2020 00:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:32:57: #1 finished! INFO @ Tue, 30 Jun 2020 00:32:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:32:59: #2 number of paired peaks: 649 WARNING @ Tue, 30 Jun 2020 00:32:59: Fewer paired peaks (649) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 649 pairs to build model! INFO @ Tue, 30 Jun 2020 00:32:59: start model_add_line... INFO @ Tue, 30 Jun 2020 00:32:59: start X-correlation... INFO @ Tue, 30 Jun 2020 00:32:59: end of X-cor INFO @ Tue, 30 Jun 2020 00:32:59: #2 finished! INFO @ Tue, 30 Jun 2020 00:32:59: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:32:59: #2 alternative fragment length(s) may be 2,18 bps INFO @ Tue, 30 Jun 2020 00:32:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.20_model.r WARNING @ Tue, 30 Jun 2020 00:32:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:32:59: #2 You may need to consider one of the other alternative d(s): 2,18 WARNING @ Tue, 30 Jun 2020 00:32:59: #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 00:32:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:32:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.05_summits.bed INFO @ Tue, 30 Jun 2020 00:33:01: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:33:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.10_summits.bed INFO @ Tue, 30 Jun 2020 00:33:24: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:33:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:33:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:33:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:33:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736607/SRX5736607.20_summits.bed INFO @ Tue, 30 Jun 2020 00:33:54: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling