Job ID = 6457507 SRX = SRX4664661 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:41:25 prefetch.2.10.7: 1) Downloading 'SRR7813088'... 2020-06-21T11:41:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:43:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:43:43 prefetch.2.10.7: 'SRR7813088' is valid 2020-06-21T11:43:43 prefetch.2.10.7: 1) 'SRR7813088' was downloaded successfully Read 21228103 spots for SRR7813088/SRR7813088.sra Written 21228103 spots for SRR7813088/SRR7813088.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: 00:06:15 21228103 reads; of these: 21228103 (100.00%) were unpaired; of these: 693562 (3.27%) aligned 0 times 13700835 (64.54%) aligned exactly 1 time 6833706 (32.19%) aligned >1 times 96.73% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 3446787 / 20534541 = 0.1679 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 20:55:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.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 20:55:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:55:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:55:30: 1000000 INFO @ Sun, 21 Jun 2020 20:55:35: 2000000 INFO @ Sun, 21 Jun 2020 20:55:40: 3000000 INFO @ Sun, 21 Jun 2020 20:55:46: 4000000 INFO @ Sun, 21 Jun 2020 20:55:51: 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 @ Sun, 21 Jun 2020 20:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.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 20:55:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:55:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:55:57: 6000000 INFO @ Sun, 21 Jun 2020 20:56:00: 1000000 INFO @ Sun, 21 Jun 2020 20:56:03: 7000000 INFO @ Sun, 21 Jun 2020 20:56:06: 2000000 INFO @ Sun, 21 Jun 2020 20:56:09: 8000000 INFO @ Sun, 21 Jun 2020 20:56:12: 3000000 INFO @ Sun, 21 Jun 2020 20:56:15: 9000000 INFO @ Sun, 21 Jun 2020 20:56:18: 4000000 INFO @ Sun, 21 Jun 2020 20:56:20: 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 @ Sun, 21 Jun 2020 20:56:24: 5000000 INFO @ Sun, 21 Jun 2020 20:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.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 20:56:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:56:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:56:26: 11000000 INFO @ Sun, 21 Jun 2020 20:56:30: 6000000 INFO @ Sun, 21 Jun 2020 20:56:30: 1000000 INFO @ Sun, 21 Jun 2020 20:56:32: 12000000 INFO @ Sun, 21 Jun 2020 20:56:36: 7000000 INFO @ Sun, 21 Jun 2020 20:56:36: 2000000 INFO @ Sun, 21 Jun 2020 20:56:38: 13000000 INFO @ Sun, 21 Jun 2020 20:56:42: 8000000 INFO @ Sun, 21 Jun 2020 20:56:42: 3000000 INFO @ Sun, 21 Jun 2020 20:56:44: 14000000 INFO @ Sun, 21 Jun 2020 20:56:48: 4000000 INFO @ Sun, 21 Jun 2020 20:56:48: 9000000 INFO @ Sun, 21 Jun 2020 20:56:50: 15000000 INFO @ Sun, 21 Jun 2020 20:56:54: 5000000 INFO @ Sun, 21 Jun 2020 20:56:54: 10000000 INFO @ Sun, 21 Jun 2020 20:56:56: 16000000 INFO @ Sun, 21 Jun 2020 20:56:59: 6000000 INFO @ Sun, 21 Jun 2020 20:57:00: 11000000 INFO @ Sun, 21 Jun 2020 20:57:02: 17000000 INFO @ Sun, 21 Jun 2020 20:57:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:57:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:57:02: #1 total tags in treatment: 17087754 INFO @ Sun, 21 Jun 2020 20:57:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:02: #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 20:57:03: #1 tags after filtering in treatment: 17087682 INFO @ Sun, 21 Jun 2020 20:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:04: #2 number of paired peaks: 1883 INFO @ Sun, 21 Jun 2020 20:57:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:04: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:57:04: #2 alternative fragment length(s) may be 2,57 bps INFO @ Sun, 21 Jun 2020 20:57:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.05_model.r WARNING @ Sun, 21 Jun 2020 20:57:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:57:04: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Sun, 21 Jun 2020 20:57:04: #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 20:57:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:05: 7000000 INFO @ Sun, 21 Jun 2020 20:57:06: 12000000 INFO @ Sun, 21 Jun 2020 20:57:11: 8000000 INFO @ Sun, 21 Jun 2020 20:57:11: 13000000 INFO @ Sun, 21 Jun 2020 20:57:17: 9000000 INFO @ Sun, 21 Jun 2020 20:57:17: 14000000 INFO @ Sun, 21 Jun 2020 20:57:22: 10000000 INFO @ Sun, 21 Jun 2020 20:57:23: 15000000 INFO @ Sun, 21 Jun 2020 20:57:28: 11000000 INFO @ Sun, 21 Jun 2020 20:57:29: 16000000 INFO @ Sun, 21 Jun 2020 20:57:33: 12000000 INFO @ Sun, 21 Jun 2020 20:57:35: 17000000 INFO @ Sun, 21 Jun 2020 20:57:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:57:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:57:36: #1 total tags in treatment: 17087754 INFO @ Sun, 21 Jun 2020 20:57:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:36: #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 20:57:36: #1 tags after filtering in treatment: 17087682 INFO @ Sun, 21 Jun 2020 20:57:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:38: #2 number of paired peaks: 1883 INFO @ Sun, 21 Jun 2020 20:57:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:38: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:57:38: #2 alternative fragment length(s) may be 2,57 bps INFO @ Sun, 21 Jun 2020 20:57:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.10_model.r WARNING @ Sun, 21 Jun 2020 20:57:38: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:57:38: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Sun, 21 Jun 2020 20:57:38: #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 20:57:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:57:39: 13000000 INFO @ Sun, 21 Jun 2020 20:57:44: 14000000 INFO @ Sun, 21 Jun 2020 20:57:50: 15000000 INFO @ Sun, 21 Jun 2020 20:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.05_summits.bed INFO @ Sun, 21 Jun 2020 20:57:52: Done! pass1 - making usageList (620 chroms): 1 millis pass2 - checking and writing primary data (3827 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:57:55: 16000000 INFO @ Sun, 21 Jun 2020 20:58:01: 17000000 INFO @ Sun, 21 Jun 2020 20:58:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:01: #1 total tags in treatment: 17087754 INFO @ Sun, 21 Jun 2020 20:58:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:01: #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 20:58:02: #1 tags after filtering in treatment: 17087682 INFO @ Sun, 21 Jun 2020 20:58:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:03: #2 number of paired peaks: 1883 INFO @ Sun, 21 Jun 2020 20:58:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:03: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:58:03: #2 alternative fragment length(s) may be 2,57 bps INFO @ Sun, 21 Jun 2020 20:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.20_model.r WARNING @ Sun, 21 Jun 2020 20:58:03: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:03: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Sun, 21 Jun 2020 20:58:03: #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 20:58:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.10_summits.bed INFO @ Sun, 21 Jun 2020 20:58:28: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (2563 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:58:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664661/SRX4664661.20_summits.bed INFO @ Sun, 21 Jun 2020 20:58:52: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (1739 records, 4 fields): 14 millis CompletedMACS2peakCalling