Job ID = 6454983 SRX = SRX2618522 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:10 prefetch.2.10.7: 1) Downloading 'SRR5319076'... 2020-06-21T09:40:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:44 prefetch.2.10.7: 'SRR5319076' is valid 2020-06-21T09:41:44 prefetch.2.10.7: 1) 'SRR5319076' was downloaded successfully 2020-06-21T09:41:44 prefetch.2.10.7: 'SRR5319076' has 0 unresolved dependencies Read 14638335 spots for SRR5319076/SRR5319076.sra Written 14638335 spots for SRR5319076/SRR5319076.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: 00:03:50 14638335 reads; of these: 14638335 (100.00%) were unpaired; of these: 735648 (5.03%) aligned 0 times 10361078 (70.78%) aligned exactly 1 time 3541609 (24.19%) aligned >1 times 94.97% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 1826624 / 13902687 = 0.1314 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 18:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.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 18:49:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:04: 1000000 INFO @ Sun, 21 Jun 2020 18:50:10: 2000000 INFO @ Sun, 21 Jun 2020 18:50:15: 3000000 INFO @ Sun, 21 Jun 2020 18:50:20: 4000000 INFO @ Sun, 21 Jun 2020 18:50:26: 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 18:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.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 18:50:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:31: 6000000 INFO @ Sun, 21 Jun 2020 18:50:36: 1000000 INFO @ Sun, 21 Jun 2020 18:50:37: 7000000 INFO @ Sun, 21 Jun 2020 18:50:42: 2000000 INFO @ Sun, 21 Jun 2020 18:50:44: 8000000 INFO @ Sun, 21 Jun 2020 18:50:49: 3000000 INFO @ Sun, 21 Jun 2020 18:50:50: 9000000 INFO @ Sun, 21 Jun 2020 18:50:56: 4000000 INFO @ Sun, 21 Jun 2020 18:50:57: 10000000 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 18:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.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 18:50:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:02: 5000000 INFO @ Sun, 21 Jun 2020 18:51:03: 11000000 INFO @ Sun, 21 Jun 2020 18:51:06: 1000000 INFO @ Sun, 21 Jun 2020 18:51:09: 6000000 INFO @ Sun, 21 Jun 2020 18:51:09: 12000000 INFO @ Sun, 21 Jun 2020 18:51:10: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:51:10: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:51:10: #1 total tags in treatment: 12076063 INFO @ Sun, 21 Jun 2020 18:51:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:10: #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 18:51:10: #1 tags after filtering in treatment: 12076061 INFO @ Sun, 21 Jun 2020 18:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:11: #2 number of paired peaks: 696 WARNING @ Sun, 21 Jun 2020 18:51:11: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:11: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:51:11: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 18:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:11: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:11: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 18:51:11: #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 18:51:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:13: 2000000 INFO @ Sun, 21 Jun 2020 18:51:16: 7000000 INFO @ Sun, 21 Jun 2020 18:51:20: 3000000 INFO @ Sun, 21 Jun 2020 18:51:22: 8000000 INFO @ Sun, 21 Jun 2020 18:51:27: 4000000 INFO @ Sun, 21 Jun 2020 18:51:29: 9000000 INFO @ Sun, 21 Jun 2020 18:51:33: 5000000 INFO @ Sun, 21 Jun 2020 18:51:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:36: 10000000 INFO @ Sun, 21 Jun 2020 18:51:40: 6000000 INFO @ Sun, 21 Jun 2020 18:51:43: 11000000 INFO @ Sun, 21 Jun 2020 18:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:46: Done! pass1 - making usageList (607 chroms): 2 millis pass2 - checking and writing primary data (5002 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:47: 7000000 INFO @ Sun, 21 Jun 2020 18:51:49: 12000000 INFO @ Sun, 21 Jun 2020 18:51:50: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:51:50: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:51:50: #1 total tags in treatment: 12076063 INFO @ Sun, 21 Jun 2020 18:51:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:50: #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 18:51:50: #1 tags after filtering in treatment: 12076061 INFO @ Sun, 21 Jun 2020 18:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:51: #2 number of paired peaks: 696 WARNING @ Sun, 21 Jun 2020 18:51:51: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:51: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:51:51: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 18:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.10_model.r WARNING @ Sun, 21 Jun 2020 18:51:51: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:51: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 18:51:51: #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 18:51:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:53: 8000000 INFO @ Sun, 21 Jun 2020 18:51:59: 9000000 INFO @ Sun, 21 Jun 2020 18:52:04: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:10: 11000000 INFO @ Sun, 21 Jun 2020 18:52:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:16: 12000000 INFO @ Sun, 21 Jun 2020 18:52:16: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:52:16: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:52:16: #1 total tags in treatment: 12076063 INFO @ Sun, 21 Jun 2020 18:52:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:16: #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 18:52:17: #1 tags after filtering in treatment: 12076061 INFO @ Sun, 21 Jun 2020 18:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:17: #2 number of paired peaks: 696 WARNING @ Sun, 21 Jun 2020 18:52:17: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:17: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:52:17: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 18:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:17: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:17: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 18:52:17: #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 18:52:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:28: Done! pass1 - making usageList (489 chroms): 1 millis pass2 - checking and writing primary data (2714 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618522/SRX2618522.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:53: Done! pass1 - making usageList (315 chroms): 0 millis pass2 - checking and writing primary data (913 records, 4 fields): 10 millis CompletedMACS2peakCalling