Job ID = 6527682 SRX = SRX2055963 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:18:05 prefetch.2.10.7: 1) Downloading 'SRR4069195'... 2020-06-29T13:18:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:20:00 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:20:00 prefetch.2.10.7: 1) 'SRR4069195' was downloaded successfully Read 24311469 spots for SRR4069195/SRR4069195.sra Written 24311469 spots for SRR4069195/SRR4069195.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: 00:09:42 24311469 reads; of these: 24311469 (100.00%) were unpaired; of these: 576430 (2.37%) aligned 0 times 15449455 (63.55%) aligned exactly 1 time 8285584 (34.08%) aligned >1 times 97.63% overall alignment rate Time searching: 00:09:42 Overall time: 00:09:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2629992 / 23735039 = 0.1108 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 22:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.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 22:41:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:29: 1000000 INFO @ Mon, 29 Jun 2020 22:41:34: 2000000 INFO @ Mon, 29 Jun 2020 22:41:40: 3000000 INFO @ Mon, 29 Jun 2020 22:41:45: 4000000 INFO @ Mon, 29 Jun 2020 22:41:51: 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 @ Mon, 29 Jun 2020 22:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.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 22:41:53: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:53: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:57: 6000000 INFO @ Mon, 29 Jun 2020 22:41:59: 1000000 INFO @ Mon, 29 Jun 2020 22:42:03: 7000000 INFO @ Mon, 29 Jun 2020 22:42:05: 2000000 INFO @ Mon, 29 Jun 2020 22:42:09: 8000000 INFO @ Mon, 29 Jun 2020 22:42:11: 3000000 INFO @ Mon, 29 Jun 2020 22:42:14: 9000000 INFO @ Mon, 29 Jun 2020 22:42:17: 4000000 INFO @ Mon, 29 Jun 2020 22:42:20: 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 @ Mon, 29 Jun 2020 22:42:23: 5000000 INFO @ Mon, 29 Jun 2020 22:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.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 22:42:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:42:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:42:26: 11000000 INFO @ Mon, 29 Jun 2020 22:42:29: 6000000 INFO @ Mon, 29 Jun 2020 22:42:29: 1000000 INFO @ Mon, 29 Jun 2020 22:42:32: 12000000 INFO @ Mon, 29 Jun 2020 22:42:35: 7000000 INFO @ Mon, 29 Jun 2020 22:42:35: 2000000 INFO @ Mon, 29 Jun 2020 22:42:38: 13000000 INFO @ Mon, 29 Jun 2020 22:42:41: 8000000 INFO @ Mon, 29 Jun 2020 22:42:41: 3000000 INFO @ Mon, 29 Jun 2020 22:42:44: 14000000 INFO @ Mon, 29 Jun 2020 22:42:47: 9000000 INFO @ Mon, 29 Jun 2020 22:42:47: 4000000 INFO @ Mon, 29 Jun 2020 22:42:50: 15000000 INFO @ Mon, 29 Jun 2020 22:42:53: 10000000 INFO @ Mon, 29 Jun 2020 22:42:53: 5000000 INFO @ Mon, 29 Jun 2020 22:42:56: 16000000 INFO @ Mon, 29 Jun 2020 22:42:59: 11000000 INFO @ Mon, 29 Jun 2020 22:43:00: 6000000 INFO @ Mon, 29 Jun 2020 22:43:01: 17000000 INFO @ Mon, 29 Jun 2020 22:43:05: 12000000 INFO @ Mon, 29 Jun 2020 22:43:06: 7000000 INFO @ Mon, 29 Jun 2020 22:43:07: 18000000 INFO @ Mon, 29 Jun 2020 22:43:11: 13000000 INFO @ Mon, 29 Jun 2020 22:43:12: 8000000 INFO @ Mon, 29 Jun 2020 22:43:13: 19000000 INFO @ Mon, 29 Jun 2020 22:43:17: 14000000 INFO @ Mon, 29 Jun 2020 22:43:17: 9000000 INFO @ Mon, 29 Jun 2020 22:43:19: 20000000 INFO @ Mon, 29 Jun 2020 22:43:23: 15000000 INFO @ Mon, 29 Jun 2020 22:43:23: 10000000 INFO @ Mon, 29 Jun 2020 22:43:25: 21000000 INFO @ Mon, 29 Jun 2020 22:43:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:43:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:43:26: #1 total tags in treatment: 21105047 INFO @ Mon, 29 Jun 2020 22:43:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:43:26: #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 22:43:26: #1 tags after filtering in treatment: 21105047 INFO @ Mon, 29 Jun 2020 22:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:43:26: #1 finished! INFO @ Mon, 29 Jun 2020 22:43:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:43:28: #2 number of paired peaks: 843 WARNING @ Mon, 29 Jun 2020 22:43:28: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Mon, 29 Jun 2020 22:43:28: start model_add_line... INFO @ Mon, 29 Jun 2020 22:43:28: start X-correlation... INFO @ Mon, 29 Jun 2020 22:43:28: end of X-cor INFO @ Mon, 29 Jun 2020 22:43:28: #2 finished! INFO @ Mon, 29 Jun 2020 22:43:28: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:43:28: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 29 Jun 2020 22:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.05_model.r WARNING @ Mon, 29 Jun 2020 22:43:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:43:28: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 29 Jun 2020 22:43:28: #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 22:43:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:43:29: 16000000 INFO @ Mon, 29 Jun 2020 22:43:29: 11000000 INFO @ Mon, 29 Jun 2020 22:43:34: 17000000 INFO @ Mon, 29 Jun 2020 22:43:35: 12000000 INFO @ Mon, 29 Jun 2020 22:43:40: 18000000 INFO @ Mon, 29 Jun 2020 22:43:41: 13000000 INFO @ Mon, 29 Jun 2020 22:43:46: 19000000 INFO @ Mon, 29 Jun 2020 22:43:47: 14000000 INFO @ Mon, 29 Jun 2020 22:43:53: 20000000 INFO @ Mon, 29 Jun 2020 22:43:53: 15000000 INFO @ Mon, 29 Jun 2020 22:43:59: 16000000 INFO @ Mon, 29 Jun 2020 22:43:59: 21000000 INFO @ Mon, 29 Jun 2020 22:44:00: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:00: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:00: #1 total tags in treatment: 21105047 INFO @ Mon, 29 Jun 2020 22:44:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:00: #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 22:44:00: #1 tags after filtering in treatment: 21105047 INFO @ Mon, 29 Jun 2020 22:44:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:00: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:01: #2 number of paired peaks: 843 WARNING @ Mon, 29 Jun 2020 22:44:01: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Mon, 29 Jun 2020 22:44:01: start model_add_line... INFO @ Mon, 29 Jun 2020 22:44:02: start X-correlation... INFO @ Mon, 29 Jun 2020 22:44:02: end of X-cor INFO @ Mon, 29 Jun 2020 22:44:02: #2 finished! INFO @ Mon, 29 Jun 2020 22:44:02: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:44:02: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 29 Jun 2020 22:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.10_model.r WARNING @ Mon, 29 Jun 2020 22:44:02: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:44:02: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 29 Jun 2020 22:44:02: #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 22:44:02: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:44:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:44:04: 17000000 INFO @ Mon, 29 Jun 2020 22:44:10: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:44:10: 18000000 INFO @ Mon, 29 Jun 2020 22:44:15: 19000000 INFO @ Mon, 29 Jun 2020 22:44:21: 20000000 INFO @ Mon, 29 Jun 2020 22:44:27: 21000000 INFO @ Mon, 29 Jun 2020 22:44:28: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:28: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:28: #1 total tags in treatment: 21105047 INFO @ Mon, 29 Jun 2020 22:44:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:28: #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 22:44:28: #1 tags after filtering in treatment: 21105047 INFO @ Mon, 29 Jun 2020 22:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:28: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:30: #2 number of paired peaks: 843 WARNING @ Mon, 29 Jun 2020 22:44:30: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Mon, 29 Jun 2020 22:44:30: start model_add_line... INFO @ Mon, 29 Jun 2020 22:44:30: start X-correlation... INFO @ Mon, 29 Jun 2020 22:44:30: end of X-cor INFO @ Mon, 29 Jun 2020 22:44:30: #2 finished! INFO @ Mon, 29 Jun 2020 22:44:30: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:44:30: #2 alternative fragment length(s) may be 2,47 bps INFO @ Mon, 29 Jun 2020 22:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.20_model.r WARNING @ Mon, 29 Jun 2020 22:44:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:44:30: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Mon, 29 Jun 2020 22:44:30: #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 22:44:30: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.05_summits.bed INFO @ Mon, 29 Jun 2020 22:44:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3928 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:44:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:45:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.10_summits.bed INFO @ Mon, 29 Jun 2020 22:45:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2866 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:45:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:45:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2055963/SRX2055963.20_summits.bed INFO @ Mon, 29 Jun 2020 22:45:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1604 records, 4 fields): 3 millis CompletedMACS2peakCalling