Job ID = 6528095 SRX = SRX4580638 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:24:52 prefetch.2.10.7: 1) Downloading 'SRR7724141'... 2020-06-29T14:24:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:35:20 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:35:20 prefetch.2.10.7: 1) 'SRR7724141' was downloaded successfully Read 58279959 spots for SRR7724141/SRR7724141.sra Written 58279959 spots for SRR7724141/SRR7724141.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: 00:00:01 Multiseed full-index search: 00:22:20 58279959 reads; of these: 58279959 (100.00%) were unpaired; of these: 17785638 (30.52%) aligned 0 times 17887391 (30.69%) aligned exactly 1 time 22606930 (38.79%) aligned >1 times 69.48% overall alignment rate Time searching: 00:22:21 Overall time: 00:22:21 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 20 files... [bam_rmdupse_core] 15418511 / 40494321 = 0.3808 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 00:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.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 00:25:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:25:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:25:06: 1000000 INFO @ Tue, 30 Jun 2020 00:25:12: 2000000 INFO @ Tue, 30 Jun 2020 00:25:18: 3000000 INFO @ Tue, 30 Jun 2020 00:25:23: 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 00:25:29: 5000000 INFO @ Tue, 30 Jun 2020 00:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.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 00:25:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:25:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:25:36: 6000000 INFO @ Tue, 30 Jun 2020 00:25:37: 1000000 INFO @ Tue, 30 Jun 2020 00:25:42: 7000000 INFO @ Tue, 30 Jun 2020 00:25:44: 2000000 INFO @ Tue, 30 Jun 2020 00:25:49: 8000000 INFO @ Tue, 30 Jun 2020 00:25:52: 3000000 INFO @ Tue, 30 Jun 2020 00:25:55: 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 00:25:59: 4000000 INFO @ Tue, 30 Jun 2020 00:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.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 00:26:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:26:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:26:02: 10000000 INFO @ Tue, 30 Jun 2020 00:26:06: 5000000 INFO @ Tue, 30 Jun 2020 00:26:07: 1000000 INFO @ Tue, 30 Jun 2020 00:26:09: 11000000 INFO @ Tue, 30 Jun 2020 00:26:14: 6000000 INFO @ Tue, 30 Jun 2020 00:26:14: 2000000 INFO @ Tue, 30 Jun 2020 00:26:16: 12000000 INFO @ Tue, 30 Jun 2020 00:26:20: 3000000 INFO @ Tue, 30 Jun 2020 00:26:21: 7000000 INFO @ Tue, 30 Jun 2020 00:26:22: 13000000 INFO @ Tue, 30 Jun 2020 00:26:27: 4000000 INFO @ Tue, 30 Jun 2020 00:26:28: 8000000 INFO @ Tue, 30 Jun 2020 00:26:29: 14000000 INFO @ Tue, 30 Jun 2020 00:26:34: 5000000 INFO @ Tue, 30 Jun 2020 00:26:36: 9000000 INFO @ Tue, 30 Jun 2020 00:26:36: 15000000 INFO @ Tue, 30 Jun 2020 00:26:41: 6000000 INFO @ Tue, 30 Jun 2020 00:26:43: 16000000 INFO @ Tue, 30 Jun 2020 00:26:43: 10000000 INFO @ Tue, 30 Jun 2020 00:26:48: 7000000 INFO @ Tue, 30 Jun 2020 00:26:50: 17000000 INFO @ Tue, 30 Jun 2020 00:26:51: 11000000 INFO @ Tue, 30 Jun 2020 00:26:54: 8000000 INFO @ Tue, 30 Jun 2020 00:26:57: 18000000 INFO @ Tue, 30 Jun 2020 00:26:59: 12000000 INFO @ Tue, 30 Jun 2020 00:27:01: 9000000 INFO @ Tue, 30 Jun 2020 00:27:04: 19000000 INFO @ Tue, 30 Jun 2020 00:27:06: 13000000 INFO @ Tue, 30 Jun 2020 00:27:08: 10000000 INFO @ Tue, 30 Jun 2020 00:27:11: 20000000 INFO @ Tue, 30 Jun 2020 00:27:14: 14000000 INFO @ Tue, 30 Jun 2020 00:27:15: 11000000 INFO @ Tue, 30 Jun 2020 00:27:18: 21000000 INFO @ Tue, 30 Jun 2020 00:27:22: 15000000 INFO @ Tue, 30 Jun 2020 00:27:22: 12000000 INFO @ Tue, 30 Jun 2020 00:27:25: 22000000 INFO @ Tue, 30 Jun 2020 00:27:29: 13000000 INFO @ Tue, 30 Jun 2020 00:27:29: 16000000 INFO @ Tue, 30 Jun 2020 00:27:32: 23000000 INFO @ Tue, 30 Jun 2020 00:27:36: 14000000 INFO @ Tue, 30 Jun 2020 00:27:37: 17000000 INFO @ Tue, 30 Jun 2020 00:27:39: 24000000 INFO @ Tue, 30 Jun 2020 00:27:43: 15000000 INFO @ Tue, 30 Jun 2020 00:27:44: 18000000 INFO @ Tue, 30 Jun 2020 00:27:46: 25000000 INFO @ Tue, 30 Jun 2020 00:27:47: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:27:47: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:27:47: #1 total tags in treatment: 25075810 INFO @ Tue, 30 Jun 2020 00:27:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:27:47: #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 00:27:47: #1 tags after filtering in treatment: 25075810 INFO @ Tue, 30 Jun 2020 00:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:27:47: #1 finished! INFO @ Tue, 30 Jun 2020 00:27:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:27:49: #2 number of paired peaks: 657 WARNING @ Tue, 30 Jun 2020 00:27:49: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 30 Jun 2020 00:27:49: start model_add_line... INFO @ Tue, 30 Jun 2020 00:27:49: start X-correlation... INFO @ Tue, 30 Jun 2020 00:27:49: end of X-cor INFO @ Tue, 30 Jun 2020 00:27:49: #2 finished! INFO @ Tue, 30 Jun 2020 00:27:49: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 00:27:49: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 30 Jun 2020 00:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.05_model.r WARNING @ Tue, 30 Jun 2020 00:27:49: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:27:49: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 30 Jun 2020 00:27:49: #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 00:27:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:27:50: 16000000 INFO @ Tue, 30 Jun 2020 00:27:52: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:27:57: 17000000 INFO @ Tue, 30 Jun 2020 00:27:59: 20000000 INFO @ Tue, 30 Jun 2020 00:28:03: 18000000 INFO @ Tue, 30 Jun 2020 00:28:06: 21000000 INFO @ Tue, 30 Jun 2020 00:28:10: 19000000 INFO @ Tue, 30 Jun 2020 00:28:14: 22000000 INFO @ Tue, 30 Jun 2020 00:28:16: 20000000 INFO @ Tue, 30 Jun 2020 00:28:21: 23000000 INFO @ Tue, 30 Jun 2020 00:28:23: 21000000 INFO @ Tue, 30 Jun 2020 00:28:29: 24000000 INFO @ Tue, 30 Jun 2020 00:28:30: 22000000 INFO @ Tue, 30 Jun 2020 00:28:36: 25000000 INFO @ Tue, 30 Jun 2020 00:28:36: 23000000 INFO @ Tue, 30 Jun 2020 00:28:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:28:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:28:37: #1 total tags in treatment: 25075810 INFO @ Tue, 30 Jun 2020 00:28:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:28:37: #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 00:28:38: #1 tags after filtering in treatment: 25075810 INFO @ Tue, 30 Jun 2020 00:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:28:38: #1 finished! INFO @ Tue, 30 Jun 2020 00:28:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:28:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:28:39: #2 number of paired peaks: 657 WARNING @ Tue, 30 Jun 2020 00:28:39: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 30 Jun 2020 00:28:39: start model_add_line... INFO @ Tue, 30 Jun 2020 00:28:40: start X-correlation... INFO @ Tue, 30 Jun 2020 00:28:40: end of X-cor INFO @ Tue, 30 Jun 2020 00:28:40: #2 finished! INFO @ Tue, 30 Jun 2020 00:28:40: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 00:28:40: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 30 Jun 2020 00:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.10_model.r WARNING @ Tue, 30 Jun 2020 00:28:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:28:40: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 30 Jun 2020 00:28:40: #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 00:28:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:28:43: 24000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:28:49: 25000000 INFO @ Tue, 30 Jun 2020 00:28:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:28:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:28:49: #1 total tags in treatment: 25075810 INFO @ Tue, 30 Jun 2020 00:28:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:28:49: #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 00:28:50: #1 tags after filtering in treatment: 25075810 INFO @ Tue, 30 Jun 2020 00:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:28:50: #1 finished! INFO @ Tue, 30 Jun 2020 00:28:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:28:52: #2 number of paired peaks: 657 WARNING @ Tue, 30 Jun 2020 00:28:52: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 30 Jun 2020 00:28:52: start model_add_line... INFO @ Tue, 30 Jun 2020 00:28:52: start X-correlation... INFO @ Tue, 30 Jun 2020 00:28:52: end of X-cor INFO @ Tue, 30 Jun 2020 00:28:52: #2 finished! INFO @ Tue, 30 Jun 2020 00:28:52: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 00:28:52: #2 alternative fragment length(s) may be 3,52 bps INFO @ Tue, 30 Jun 2020 00:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.20_model.r WARNING @ Tue, 30 Jun 2020 00:28:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:28:52: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Tue, 30 Jun 2020 00:28:52: #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 00:28:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.05_summits.bed INFO @ Tue, 30 Jun 2020 00:29:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10421 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:29:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:29:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.10_summits.bed INFO @ Tue, 30 Jun 2020 00:29:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4522 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4580638/SRX4580638.20_summits.bed INFO @ Tue, 30 Jun 2020 00:30:09: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1740 records, 4 fields): 4 millis CompletedMACS2peakCalling