Job ID = 6527886 SRX = SRX306200 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:21:50 prefetch.2.10.7: 1) Downloading 'SRR901303'... 2020-06-29T14:21:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:26:16 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:26:16 prefetch.2.10.7: 1) 'SRR901303' was downloaded successfully Read 30896823 spots for SRR901303/SRR901303.sra Written 30896823 spots for SRR901303/SRR901303.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: 00:12:14 30896823 reads; of these: 30896823 (100.00%) were unpaired; of these: 976945 (3.16%) aligned 0 times 20035523 (64.85%) aligned exactly 1 time 9884355 (31.99%) aligned >1 times 96.84% overall alignment rate Time searching: 00:12:14 Overall time: 00:12:14 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 16 files... [bam_rmdupse_core] 3921411 / 29919878 = 0.1311 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 @ Mon, 29 Jun 2020 23:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.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 @ Mon, 29 Jun 2020 23:56:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:56:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:56:50: 1000000 INFO @ Mon, 29 Jun 2020 23:56:56: 2000000 INFO @ Mon, 29 Jun 2020 23:57:01: 3000000 INFO @ Mon, 29 Jun 2020 23:57:07: 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 @ Mon, 29 Jun 2020 23:57:13: 5000000 INFO @ Mon, 29 Jun 2020 23:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.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 @ Mon, 29 Jun 2020 23:57:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:57:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:57:20: 6000000 INFO @ Mon, 29 Jun 2020 23:57:21: 1000000 INFO @ Mon, 29 Jun 2020 23:57:27: 7000000 INFO @ Mon, 29 Jun 2020 23:57:28: 2000000 INFO @ Mon, 29 Jun 2020 23:57:34: 8000000 INFO @ Mon, 29 Jun 2020 23:57:35: 3000000 INFO @ Mon, 29 Jun 2020 23:57:41: 9000000 INFO @ Mon, 29 Jun 2020 23:57:42: 4000000 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 @ Mon, 29 Jun 2020 23:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.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 @ Mon, 29 Jun 2020 23:57:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:57:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:57:48: 10000000 INFO @ Mon, 29 Jun 2020 23:57:49: 5000000 INFO @ Mon, 29 Jun 2020 23:57:52: 1000000 INFO @ Mon, 29 Jun 2020 23:57:55: 11000000 INFO @ Mon, 29 Jun 2020 23:57:56: 6000000 INFO @ Mon, 29 Jun 2020 23:57:59: 2000000 INFO @ Mon, 29 Jun 2020 23:58:02: 12000000 INFO @ Mon, 29 Jun 2020 23:58:04: 7000000 INFO @ Mon, 29 Jun 2020 23:58:06: 3000000 INFO @ Mon, 29 Jun 2020 23:58:10: 13000000 INFO @ Mon, 29 Jun 2020 23:58:11: 8000000 INFO @ Mon, 29 Jun 2020 23:58:14: 4000000 INFO @ Mon, 29 Jun 2020 23:58:17: 14000000 INFO @ Mon, 29 Jun 2020 23:58:18: 9000000 INFO @ Mon, 29 Jun 2020 23:58:21: 5000000 INFO @ Mon, 29 Jun 2020 23:58:24: 15000000 INFO @ Mon, 29 Jun 2020 23:58:26: 10000000 INFO @ Mon, 29 Jun 2020 23:58:29: 6000000 INFO @ Mon, 29 Jun 2020 23:58:32: 16000000 INFO @ Mon, 29 Jun 2020 23:58:33: 11000000 INFO @ Mon, 29 Jun 2020 23:58:36: 7000000 INFO @ Mon, 29 Jun 2020 23:58:39: 17000000 INFO @ Mon, 29 Jun 2020 23:58:40: 12000000 INFO @ Mon, 29 Jun 2020 23:58:43: 8000000 INFO @ Mon, 29 Jun 2020 23:58:46: 18000000 INFO @ Mon, 29 Jun 2020 23:58:47: 13000000 INFO @ Mon, 29 Jun 2020 23:58:51: 9000000 INFO @ Mon, 29 Jun 2020 23:58:53: 19000000 INFO @ Mon, 29 Jun 2020 23:58:54: 14000000 INFO @ Mon, 29 Jun 2020 23:58:58: 10000000 INFO @ Mon, 29 Jun 2020 23:59:01: 20000000 INFO @ Mon, 29 Jun 2020 23:59:02: 15000000 INFO @ Mon, 29 Jun 2020 23:59:06: 11000000 INFO @ Mon, 29 Jun 2020 23:59:08: 21000000 INFO @ Mon, 29 Jun 2020 23:59:09: 16000000 INFO @ Mon, 29 Jun 2020 23:59:13: 12000000 INFO @ Mon, 29 Jun 2020 23:59:15: 22000000 INFO @ Mon, 29 Jun 2020 23:59:16: 17000000 INFO @ Mon, 29 Jun 2020 23:59:20: 13000000 INFO @ Mon, 29 Jun 2020 23:59:22: 23000000 INFO @ Mon, 29 Jun 2020 23:59:23: 18000000 INFO @ Mon, 29 Jun 2020 23:59:27: 14000000 INFO @ Mon, 29 Jun 2020 23:59:29: 24000000 INFO @ Mon, 29 Jun 2020 23:59:30: 19000000 INFO @ Mon, 29 Jun 2020 23:59:34: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:59:37: 25000000 INFO @ Mon, 29 Jun 2020 23:59:37: 20000000 INFO @ Mon, 29 Jun 2020 23:59:42: 16000000 INFO @ Mon, 29 Jun 2020 23:59:44: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:59:44: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:59:44: #1 total tags in treatment: 25998467 INFO @ Mon, 29 Jun 2020 23:59:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:59:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:59:44: #1 tags after filtering in treatment: 25998467 INFO @ Mon, 29 Jun 2020 23:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:59:44: #1 finished! INFO @ Mon, 29 Jun 2020 23:59:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:59:44: 21000000 INFO @ Mon, 29 Jun 2020 23:59:46: #2 number of paired peaks: 249 WARNING @ Mon, 29 Jun 2020 23:59:46: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Mon, 29 Jun 2020 23:59:46: start model_add_line... INFO @ Mon, 29 Jun 2020 23:59:46: start X-correlation... INFO @ Mon, 29 Jun 2020 23:59:46: end of X-cor INFO @ Mon, 29 Jun 2020 23:59:46: #2 finished! INFO @ Mon, 29 Jun 2020 23:59:46: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 23:59:46: #2 alternative fragment length(s) may be 2,51,522,543 bps INFO @ Mon, 29 Jun 2020 23:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.05_model.r WARNING @ Mon, 29 Jun 2020 23:59:46: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:59:46: #2 You may need to consider one of the other alternative d(s): 2,51,522,543 WARNING @ Mon, 29 Jun 2020 23:59:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:59:46: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:59:49: 17000000 INFO @ Mon, 29 Jun 2020 23:59:51: 22000000 INFO @ Mon, 29 Jun 2020 23:59:55: 18000000 INFO @ Mon, 29 Jun 2020 23:59:58: 23000000 INFO @ Tue, 30 Jun 2020 00:00:03: 19000000 INFO @ Tue, 30 Jun 2020 00:00:05: 24000000 INFO @ Tue, 30 Jun 2020 00:00:09: 20000000 INFO @ Tue, 30 Jun 2020 00:00:11: 25000000 INFO @ Tue, 30 Jun 2020 00:00:16: 21000000 INFO @ Tue, 30 Jun 2020 00:00:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:00:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:00:18: #1 total tags in treatment: 25998467 INFO @ Tue, 30 Jun 2020 00:00:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:18: #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 00:00:18: #1 tags after filtering in treatment: 25998467 INFO @ Tue, 30 Jun 2020 00:00:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:00:18: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:20: #2 number of paired peaks: 249 WARNING @ Tue, 30 Jun 2020 00:00:20: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 30 Jun 2020 00:00:20: start model_add_line... INFO @ Tue, 30 Jun 2020 00:00:20: start X-correlation... INFO @ Tue, 30 Jun 2020 00:00:20: end of X-cor INFO @ Tue, 30 Jun 2020 00:00:20: #2 finished! INFO @ Tue, 30 Jun 2020 00:00:20: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 00:00:20: #2 alternative fragment length(s) may be 2,51,522,543 bps INFO @ Tue, 30 Jun 2020 00:00:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.10_model.r WARNING @ Tue, 30 Jun 2020 00:00:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:00:20: #2 You may need to consider one of the other alternative d(s): 2,51,522,543 WARNING @ Tue, 30 Jun 2020 00:00:20: #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 00:00:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:00:22: 22000000 INFO @ Tue, 30 Jun 2020 00:00:29: 23000000 INFO @ Tue, 30 Jun 2020 00:00:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:00:34: 24000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:00:40: 25000000 INFO @ Tue, 30 Jun 2020 00:00:46: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:00:46: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:00:46: #1 total tags in treatment: 25998467 INFO @ Tue, 30 Jun 2020 00:00:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:46: #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 00:00:47: #1 tags after filtering in treatment: 25998467 INFO @ Tue, 30 Jun 2020 00:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:00:47: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:48: #2 number of paired peaks: 249 WARNING @ Tue, 30 Jun 2020 00:00:48: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 30 Jun 2020 00:00:48: start model_add_line... INFO @ Tue, 30 Jun 2020 00:00:48: start X-correlation... INFO @ Tue, 30 Jun 2020 00:00:48: end of X-cor INFO @ Tue, 30 Jun 2020 00:00:48: #2 finished! INFO @ Tue, 30 Jun 2020 00:00:48: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 00:00:48: #2 alternative fragment length(s) may be 2,51,522,543 bps INFO @ Tue, 30 Jun 2020 00:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.20_model.r WARNING @ Tue, 30 Jun 2020 00:00:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:00:48: #2 You may need to consider one of the other alternative d(s): 2,51,522,543 WARNING @ Tue, 30 Jun 2020 00:00:48: #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 00:00:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.05_summits.bed INFO @ Tue, 30 Jun 2020 00:00:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3708 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:01:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.10_summits.bed INFO @ Tue, 30 Jun 2020 00:01:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2493 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:01:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:01:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:01:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:01:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306200/SRX306200.20_summits.bed INFO @ Tue, 30 Jun 2020 00:01:55: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1220 records, 4 fields): 3 millis CompletedMACS2peakCalling