Job ID = 6457510 SRX = SRX4664662 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:44:48 prefetch.2.10.7: 1) Downloading 'SRR7813089'... 2020-06-21T11:44:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:48:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:48:51 prefetch.2.10.7: 1) 'SRR7813089' was downloaded successfully Read 28779797 spots for SRR7813089/SRR7813089.sra Written 28779797 spots for SRR7813089/SRR7813089.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: 00:08:42 28779797 reads; of these: 28779797 (100.00%) were unpaired; of these: 886652 (3.08%) aligned 0 times 18643316 (64.78%) aligned exactly 1 time 9249829 (32.14%) aligned >1 times 96.92% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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] 4712168 / 27893145 = 0.1689 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 21:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.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 21:04:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:04:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:39: 1000000 INFO @ Sun, 21 Jun 2020 21:04:44: 2000000 INFO @ Sun, 21 Jun 2020 21:04:48: 3000000 INFO @ Sun, 21 Jun 2020 21:04:53: 4000000 INFO @ Sun, 21 Jun 2020 21:04:58: 5000000 INFO @ Sun, 21 Jun 2020 21:05:02: 6000000 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 21:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.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 21:05:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:07: 7000000 INFO @ Sun, 21 Jun 2020 21:05:09: 1000000 INFO @ Sun, 21 Jun 2020 21:05:12: 8000000 INFO @ Sun, 21 Jun 2020 21:05:14: 2000000 INFO @ Sun, 21 Jun 2020 21:05:17: 9000000 INFO @ Sun, 21 Jun 2020 21:05:19: 3000000 INFO @ Sun, 21 Jun 2020 21:05:21: 10000000 INFO @ Sun, 21 Jun 2020 21:05:23: 4000000 INFO @ Sun, 21 Jun 2020 21:05:26: 11000000 INFO @ Sun, 21 Jun 2020 21:05:28: 5000000 INFO @ Sun, 21 Jun 2020 21:05:31: 12000000 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 21:05:33: 6000000 INFO @ Sun, 21 Jun 2020 21:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.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 21:05:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:36: 13000000 INFO @ Sun, 21 Jun 2020 21:05:38: 7000000 INFO @ Sun, 21 Jun 2020 21:05:39: 1000000 INFO @ Sun, 21 Jun 2020 21:05:41: 14000000 INFO @ Sun, 21 Jun 2020 21:05:43: 8000000 INFO @ Sun, 21 Jun 2020 21:05:44: 2000000 INFO @ Sun, 21 Jun 2020 21:05:46: 15000000 INFO @ Sun, 21 Jun 2020 21:05:47: 9000000 INFO @ Sun, 21 Jun 2020 21:05:49: 3000000 INFO @ Sun, 21 Jun 2020 21:05:50: 16000000 INFO @ Sun, 21 Jun 2020 21:05:52: 10000000 INFO @ Sun, 21 Jun 2020 21:05:54: 4000000 INFO @ Sun, 21 Jun 2020 21:05:55: 17000000 INFO @ Sun, 21 Jun 2020 21:05:57: 11000000 INFO @ Sun, 21 Jun 2020 21:05:59: 5000000 INFO @ Sun, 21 Jun 2020 21:06:00: 18000000 INFO @ Sun, 21 Jun 2020 21:06:02: 12000000 INFO @ Sun, 21 Jun 2020 21:06:03: 6000000 INFO @ Sun, 21 Jun 2020 21:06:05: 19000000 INFO @ Sun, 21 Jun 2020 21:06:07: 13000000 INFO @ Sun, 21 Jun 2020 21:06:08: 7000000 INFO @ Sun, 21 Jun 2020 21:06:10: 20000000 INFO @ Sun, 21 Jun 2020 21:06:12: 14000000 INFO @ Sun, 21 Jun 2020 21:06:13: 8000000 INFO @ Sun, 21 Jun 2020 21:06:15: 21000000 INFO @ Sun, 21 Jun 2020 21:06:16: 15000000 INFO @ Sun, 21 Jun 2020 21:06:18: 9000000 INFO @ Sun, 21 Jun 2020 21:06:20: 22000000 INFO @ Sun, 21 Jun 2020 21:06:21: 16000000 INFO @ Sun, 21 Jun 2020 21:06:23: 10000000 INFO @ Sun, 21 Jun 2020 21:06:25: 23000000 INFO @ Sun, 21 Jun 2020 21:06:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:06:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:06:26: #1 total tags in treatment: 23180977 INFO @ Sun, 21 Jun 2020 21:06:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:26: #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 21:06:26: 17000000 INFO @ Sun, 21 Jun 2020 21:06:27: #1 tags after filtering in treatment: 23180923 INFO @ Sun, 21 Jun 2020 21:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:28: 11000000 INFO @ Sun, 21 Jun 2020 21:06:28: #2 number of paired peaks: 941 WARNING @ Sun, 21 Jun 2020 21:06:28: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Sun, 21 Jun 2020 21:06:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:28: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:06:28: #2 alternative fragment length(s) may be 1,52 bps INFO @ Sun, 21 Jun 2020 21:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.05_model.r WARNING @ Sun, 21 Jun 2020 21:06:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:06:28: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Sun, 21 Jun 2020 21:06:28: #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 21:06:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:06:31: 18000000 INFO @ Sun, 21 Jun 2020 21:06:33: 12000000 INFO @ Sun, 21 Jun 2020 21:06:36: 19000000 INFO @ Sun, 21 Jun 2020 21:06:38: 13000000 INFO @ Sun, 21 Jun 2020 21:06:41: 20000000 INFO @ Sun, 21 Jun 2020 21:06:42: 14000000 INFO @ Sun, 21 Jun 2020 21:06:46: 21000000 INFO @ Sun, 21 Jun 2020 21:06:47: 15000000 INFO @ Sun, 21 Jun 2020 21:06:51: 22000000 INFO @ Sun, 21 Jun 2020 21:06:52: 16000000 INFO @ Sun, 21 Jun 2020 21:06:56: 23000000 INFO @ Sun, 21 Jun 2020 21:06:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:06:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:06:57: #1 total tags in treatment: 23180977 INFO @ Sun, 21 Jun 2020 21:06:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:57: #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 21:06:57: 17000000 INFO @ Sun, 21 Jun 2020 21:06:58: #1 tags after filtering in treatment: 23180923 INFO @ Sun, 21 Jun 2020 21:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:59: #2 number of paired peaks: 941 WARNING @ Sun, 21 Jun 2020 21:06:59: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Sun, 21 Jun 2020 21:06:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:59: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:06:59: #2 alternative fragment length(s) may be 1,52 bps INFO @ Sun, 21 Jun 2020 21:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.10_model.r WARNING @ Sun, 21 Jun 2020 21:06:59: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:06:59: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Sun, 21 Jun 2020 21:06:59: #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 21:06:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:02: 18000000 INFO @ Sun, 21 Jun 2020 21:07:07: 19000000 INFO @ Sun, 21 Jun 2020 21:07:09: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:07:12: 20000000 INFO @ Sun, 21 Jun 2020 21:07:17: 21000000 INFO @ Sun, 21 Jun 2020 21:07:22: 22000000 INFO @ Sun, 21 Jun 2020 21:07:26: 23000000 INFO @ Sun, 21 Jun 2020 21:07:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:28: #1 total tags in treatment: 23180977 INFO @ Sun, 21 Jun 2020 21:07:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:28: #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 21:07:28: #1 tags after filtering in treatment: 23180923 INFO @ Sun, 21 Jun 2020 21:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.05_summits.bed INFO @ Sun, 21 Jun 2020 21:07:29: Done! pass1 - making usageList (664 chroms): 2 millis pass2 - checking and writing primary data (4071 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:07:30: #2 number of paired peaks: 941 WARNING @ Sun, 21 Jun 2020 21:07:30: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Sun, 21 Jun 2020 21:07:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:30: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:07:30: #2 alternative fragment length(s) may be 1,52 bps INFO @ Sun, 21 Jun 2020 21:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.20_model.r WARNING @ Sun, 21 Jun 2020 21:07:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:30: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Sun, 21 Jun 2020 21:07:30: #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 21:07:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.10_summits.bed INFO @ Sun, 21 Jun 2020 21:08:00: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (2384 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:08:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664662/SRX4664662.20_summits.bed INFO @ Sun, 21 Jun 2020 21:08:32: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (1144 records, 4 fields): 12 millis CompletedMACS2peakCalling