Job ID = 6454658 SRX = SRX245835 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:20:09 prefetch.2.10.7: 1) Downloading 'SRR765855'... 2020-06-21T09:20:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:53 prefetch.2.10.7: 'SRR765855' is valid 2020-06-21T09:22:53 prefetch.2.10.7: 1) 'SRR765855' was downloaded successfully Read 23856700 spots for SRR765855/SRR765855.sra Written 23856700 spots for SRR765855/SRR765855.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: 00:05:19 23856700 reads; of these: 23856700 (100.00%) were unpaired; of these: 985039 (4.13%) aligned 0 times 18102897 (75.88%) aligned exactly 1 time 4768764 (19.99%) aligned >1 times 95.87% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 8 files... [bam_rmdupse_core] 2223541 / 22871661 = 0.0972 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 18:34:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.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 18:34:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:26: 1000000 INFO @ Sun, 21 Jun 2020 18:34:31: 2000000 INFO @ Sun, 21 Jun 2020 18:34:36: 3000000 INFO @ Sun, 21 Jun 2020 18:34:41: 4000000 INFO @ Sun, 21 Jun 2020 18:34:46: 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 @ Sun, 21 Jun 2020 18:34:51: 6000000 INFO @ Sun, 21 Jun 2020 18:34:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.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 18:34:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:55: 7000000 INFO @ Sun, 21 Jun 2020 18:34:57: 1000000 INFO @ Sun, 21 Jun 2020 18:35:01: 8000000 INFO @ Sun, 21 Jun 2020 18:35:02: 2000000 INFO @ Sun, 21 Jun 2020 18:35:06: 9000000 INFO @ Sun, 21 Jun 2020 18:35:07: 3000000 INFO @ Sun, 21 Jun 2020 18:35:11: 10000000 INFO @ Sun, 21 Jun 2020 18:35:12: 4000000 INFO @ Sun, 21 Jun 2020 18:35:16: 11000000 INFO @ Sun, 21 Jun 2020 18:35:17: 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 18:35:21: 12000000 INFO @ Sun, 21 Jun 2020 18:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.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 18:35:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:22: 6000000 INFO @ Sun, 21 Jun 2020 18:35:26: 13000000 INFO @ Sun, 21 Jun 2020 18:35:27: 1000000 INFO @ Sun, 21 Jun 2020 18:35:27: 7000000 INFO @ Sun, 21 Jun 2020 18:35:31: 14000000 INFO @ Sun, 21 Jun 2020 18:35:33: 8000000 INFO @ Sun, 21 Jun 2020 18:35:33: 2000000 INFO @ Sun, 21 Jun 2020 18:35:37: 15000000 INFO @ Sun, 21 Jun 2020 18:35:38: 9000000 INFO @ Sun, 21 Jun 2020 18:35:39: 3000000 INFO @ Sun, 21 Jun 2020 18:35:42: 16000000 INFO @ Sun, 21 Jun 2020 18:35:43: 10000000 INFO @ Sun, 21 Jun 2020 18:35:44: 4000000 INFO @ Sun, 21 Jun 2020 18:35:48: 17000000 INFO @ Sun, 21 Jun 2020 18:35:48: 11000000 INFO @ Sun, 21 Jun 2020 18:35:50: 5000000 INFO @ Sun, 21 Jun 2020 18:35:53: 18000000 INFO @ Sun, 21 Jun 2020 18:35:53: 12000000 INFO @ Sun, 21 Jun 2020 18:35:56: 6000000 INFO @ Sun, 21 Jun 2020 18:35:58: 19000000 INFO @ Sun, 21 Jun 2020 18:35:58: 13000000 INFO @ Sun, 21 Jun 2020 18:36:02: 7000000 INFO @ Sun, 21 Jun 2020 18:36:03: 20000000 INFO @ Sun, 21 Jun 2020 18:36:04: 14000000 INFO @ Sun, 21 Jun 2020 18:36:07: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:36:07: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:36:07: #1 total tags in treatment: 20648120 INFO @ Sun, 21 Jun 2020 18:36:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:07: #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 18:36:08: #1 tags after filtering in treatment: 20648070 INFO @ Sun, 21 Jun 2020 18:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:08: 8000000 INFO @ Sun, 21 Jun 2020 18:36:09: 15000000 INFO @ Sun, 21 Jun 2020 18:36:09: #2 number of paired peaks: 217 WARNING @ Sun, 21 Jun 2020 18:36:09: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:09: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:36:09: #2 alternative fragment length(s) may be 2,21,38,582 bps INFO @ Sun, 21 Jun 2020 18:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.05_model.r WARNING @ Sun, 21 Jun 2020 18:36:09: #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 18:36:09: #2 You may need to consider one of the other alternative d(s): 2,21,38,582 WARNING @ Sun, 21 Jun 2020 18:36:09: #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 18:36:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:13: 9000000 INFO @ Sun, 21 Jun 2020 18:36:14: 16000000 INFO @ Sun, 21 Jun 2020 18:36:19: 10000000 INFO @ Sun, 21 Jun 2020 18:36:20: 17000000 INFO @ Sun, 21 Jun 2020 18:36:25: 18000000 INFO @ Sun, 21 Jun 2020 18:36:25: 11000000 INFO @ Sun, 21 Jun 2020 18:36:30: 19000000 INFO @ Sun, 21 Jun 2020 18:36:31: 12000000 INFO @ Sun, 21 Jun 2020 18:36:35: 20000000 INFO @ Sun, 21 Jun 2020 18:36:36: 13000000 INFO @ Sun, 21 Jun 2020 18:36:39: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:36:39: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:36:39: #1 total tags in treatment: 20648120 INFO @ Sun, 21 Jun 2020 18:36:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:39: #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 18:36:40: #1 tags after filtering in treatment: 20648070 INFO @ Sun, 21 Jun 2020 18:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:41: #2 number of paired peaks: 217 WARNING @ Sun, 21 Jun 2020 18:36:41: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:41: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:36:41: #2 alternative fragment length(s) may be 2,21,38,582 bps INFO @ Sun, 21 Jun 2020 18:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.10_model.r WARNING @ Sun, 21 Jun 2020 18:36:41: #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 18:36:41: #2 You may need to consider one of the other alternative d(s): 2,21,38,582 WARNING @ Sun, 21 Jun 2020 18:36:41: #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 18:36:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:42: 14000000 INFO @ Sun, 21 Jun 2020 18:36:48: 15000000 INFO @ Sun, 21 Jun 2020 18:36:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:36:59: 17000000 INFO @ Sun, 21 Jun 2020 18:37:05: 18000000 INFO @ Sun, 21 Jun 2020 18:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.05_summits.bed INFO @ Sun, 21 Jun 2020 18:37:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:37:10: 19000000 INFO @ Sun, 21 Jun 2020 18:37:16: 20000000 INFO @ Sun, 21 Jun 2020 18:37:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:20: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:37:20: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:37:20: #1 total tags in treatment: 20648120 INFO @ Sun, 21 Jun 2020 18:37:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:20: #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 18:37:20: #1 tags after filtering in treatment: 20648070 INFO @ Sun, 21 Jun 2020 18:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:22: #2 number of paired peaks: 217 WARNING @ Sun, 21 Jun 2020 18:37:22: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:22: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:37:22: #2 alternative fragment length(s) may be 2,21,38,582 bps INFO @ Sun, 21 Jun 2020 18:37:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.20_model.r WARNING @ Sun, 21 Jun 2020 18:37:22: #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 18:37:22: #2 You may need to consider one of the other alternative d(s): 2,21,38,582 WARNING @ Sun, 21 Jun 2020 18:37:22: #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 18:37:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:38:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX245835/SRX245835.20_summits.bed INFO @ Sun, 21 Jun 2020 18:38:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling