Job ID = 6497711 SRX = SRX1056722 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:44:28 prefetch.2.10.7: 1) Downloading 'SRR2060656'... 2020-06-25T22:44:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:07:50 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:07:50 prefetch.2.10.7: 1) 'SRR2060656' was downloaded successfully Read 72722084 spots for SRR2060656/SRR2060656.sra Written 72722084 spots for SRR2060656/SRR2060656.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: 04:15:48 72722084 reads; of these: 72722084 (100.00%) were paired; of these: 9475642 (13.03%) aligned concordantly 0 times 43201227 (59.41%) aligned concordantly exactly 1 time 20045215 (27.56%) aligned concordantly >1 times ---- 9475642 pairs aligned concordantly 0 times; of these: 957643 (10.11%) aligned discordantly 1 time ---- 8517999 pairs aligned 0 times concordantly or discordantly; of these: 17035998 mates make up the pairs; of these: 14437838 (84.75%) aligned 0 times 1306855 (7.67%) aligned exactly 1 time 1291305 (7.58%) aligned >1 times 90.07% overall alignment rate Time searching: 04:15:48 Overall time: 04:15:48 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 56 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 54043287 / 63965818 = 0.8449 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 @ Fri, 26 Jun 2020 13:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.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 @ Fri, 26 Jun 2020 13:14:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 13:14:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 13:14:07: 1000000 INFO @ Fri, 26 Jun 2020 13:14:14: 2000000 INFO @ Fri, 26 Jun 2020 13:14:20: 3000000 INFO @ Fri, 26 Jun 2020 13:14:27: 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 @ Fri, 26 Jun 2020 13:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.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 @ Fri, 26 Jun 2020 13:14:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 13:14:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 13:14:33: 5000000 INFO @ Fri, 26 Jun 2020 13:14:38: 1000000 INFO @ Fri, 26 Jun 2020 13:14:40: 6000000 INFO @ Fri, 26 Jun 2020 13:14:44: 2000000 INFO @ Fri, 26 Jun 2020 13:14:47: 7000000 INFO @ Fri, 26 Jun 2020 13:14:51: 3000000 INFO @ Fri, 26 Jun 2020 13:14:53: 8000000 INFO @ Fri, 26 Jun 2020 13:14:57: 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 @ Fri, 26 Jun 2020 13:15:00: 9000000 INFO @ Fri, 26 Jun 2020 13:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.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 @ Fri, 26 Jun 2020 13:15:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 13:15:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 13:15:04: 5000000 INFO @ Fri, 26 Jun 2020 13:15:07: 10000000 INFO @ Fri, 26 Jun 2020 13:15:08: 1000000 INFO @ Fri, 26 Jun 2020 13:15:11: 6000000 INFO @ Fri, 26 Jun 2020 13:15:14: 11000000 INFO @ Fri, 26 Jun 2020 13:15:15: 2000000 INFO @ Fri, 26 Jun 2020 13:15:17: 7000000 INFO @ Fri, 26 Jun 2020 13:15:21: 12000000 INFO @ Fri, 26 Jun 2020 13:15:21: 3000000 INFO @ Fri, 26 Jun 2020 13:15:24: 8000000 INFO @ Fri, 26 Jun 2020 13:15:28: 13000000 INFO @ Fri, 26 Jun 2020 13:15:28: 4000000 INFO @ Fri, 26 Jun 2020 13:15:31: 9000000 INFO @ Fri, 26 Jun 2020 13:15:35: 14000000 INFO @ Fri, 26 Jun 2020 13:15:35: 5000000 INFO @ Fri, 26 Jun 2020 13:15:38: 10000000 INFO @ Fri, 26 Jun 2020 13:15:42: 15000000 INFO @ Fri, 26 Jun 2020 13:15:42: 6000000 INFO @ Fri, 26 Jun 2020 13:15:44: 11000000 INFO @ Fri, 26 Jun 2020 13:15:48: 7000000 INFO @ Fri, 26 Jun 2020 13:15:49: 16000000 INFO @ Fri, 26 Jun 2020 13:15:51: 12000000 INFO @ Fri, 26 Jun 2020 13:15:55: 8000000 INFO @ Fri, 26 Jun 2020 13:15:55: 17000000 INFO @ Fri, 26 Jun 2020 13:15:58: 13000000 INFO @ Fri, 26 Jun 2020 13:16:02: 9000000 INFO @ Fri, 26 Jun 2020 13:16:02: 18000000 INFO @ Fri, 26 Jun 2020 13:16:04: 14000000 INFO @ Fri, 26 Jun 2020 13:16:08: 10000000 INFO @ Fri, 26 Jun 2020 13:16:09: 19000000 INFO @ Fri, 26 Jun 2020 13:16:11: 15000000 INFO @ Fri, 26 Jun 2020 13:16:15: 11000000 INFO @ Fri, 26 Jun 2020 13:16:16: 20000000 INFO @ Fri, 26 Jun 2020 13:16:17: 16000000 INFO @ Fri, 26 Jun 2020 13:16:22: 12000000 INFO @ Fri, 26 Jun 2020 13:16:23: 21000000 INFO @ Fri, 26 Jun 2020 13:16:24: 17000000 INFO @ Fri, 26 Jun 2020 13:16:28: 13000000 INFO @ Fri, 26 Jun 2020 13:16:30: 22000000 INFO @ Fri, 26 Jun 2020 13:16:31: 18000000 INFO @ Fri, 26 Jun 2020 13:16:35: 14000000 INFO @ Fri, 26 Jun 2020 13:16:36: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 13:16:36: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 13:16:36: #1 total tags in treatment: 10071486 INFO @ Fri, 26 Jun 2020 13:16:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 13:16:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 13:16:37: #1 tags after filtering in treatment: 7694880 INFO @ Fri, 26 Jun 2020 13:16:37: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 26 Jun 2020 13:16:37: #1 finished! INFO @ Fri, 26 Jun 2020 13:16:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 13:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 13:16:37: 19000000 INFO @ Fri, 26 Jun 2020 13:16:38: #2 number of paired peaks: 7515 INFO @ Fri, 26 Jun 2020 13:16:38: start model_add_line... INFO @ Fri, 26 Jun 2020 13:16:38: start X-correlation... INFO @ Fri, 26 Jun 2020 13:16:38: end of X-cor INFO @ Fri, 26 Jun 2020 13:16:38: #2 finished! INFO @ Fri, 26 Jun 2020 13:16:38: #2 predicted fragment length is 169 bps INFO @ Fri, 26 Jun 2020 13:16:38: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 26 Jun 2020 13:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.05_model.r WARNING @ Fri, 26 Jun 2020 13:16:38: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 13:16:38: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Fri, 26 Jun 2020 13:16:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 13:16:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 13:16:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 13:16:42: 15000000 INFO @ Fri, 26 Jun 2020 13:16:44: 20000000 INFO @ Fri, 26 Jun 2020 13:16:48: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 13:16:51: 21000000 INFO @ Fri, 26 Jun 2020 13:16:55: 17000000 INFO @ Fri, 26 Jun 2020 13:16:58: 22000000 INFO @ Fri, 26 Jun 2020 13:17:02: 18000000 INFO @ Fri, 26 Jun 2020 13:17:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 13:17:04: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 13:17:04: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 13:17:04: #1 total tags in treatment: 10071486 INFO @ Fri, 26 Jun 2020 13:17:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 13:17:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 13:17:04: #1 tags after filtering in treatment: 7694880 INFO @ Fri, 26 Jun 2020 13:17:04: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 26 Jun 2020 13:17:04: #1 finished! INFO @ Fri, 26 Jun 2020 13:17:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 13:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 13:17:05: #2 number of paired peaks: 7515 INFO @ Fri, 26 Jun 2020 13:17:05: start model_add_line... INFO @ Fri, 26 Jun 2020 13:17:05: start X-correlation... INFO @ Fri, 26 Jun 2020 13:17:05: end of X-cor INFO @ Fri, 26 Jun 2020 13:17:05: #2 finished! INFO @ Fri, 26 Jun 2020 13:17:05: #2 predicted fragment length is 169 bps INFO @ Fri, 26 Jun 2020 13:17:05: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 26 Jun 2020 13:17:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.10_model.r WARNING @ Fri, 26 Jun 2020 13:17:05: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 13:17:05: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Fri, 26 Jun 2020 13:17:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 13:17:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 13:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 13:17:08: 19000000 INFO @ Fri, 26 Jun 2020 13:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.05_peaks.xls INFO @ Fri, 26 Jun 2020 13:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 13:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.05_summits.bed INFO @ Fri, 26 Jun 2020 13:17:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11590 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 13:17:15: 20000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 13:17:22: 21000000 INFO @ Fri, 26 Jun 2020 13:17:28: 22000000 INFO @ Fri, 26 Jun 2020 13:17:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 13:17:34: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 13:17:34: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 13:17:34: #1 total tags in treatment: 10071486 INFO @ Fri, 26 Jun 2020 13:17:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 13:17:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 13:17:34: #1 tags after filtering in treatment: 7694880 INFO @ Fri, 26 Jun 2020 13:17:34: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 26 Jun 2020 13:17:34: #1 finished! INFO @ Fri, 26 Jun 2020 13:17:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 13:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 13:17:35: #2 number of paired peaks: 7515 INFO @ Fri, 26 Jun 2020 13:17:35: start model_add_line... INFO @ Fri, 26 Jun 2020 13:17:35: start X-correlation... INFO @ Fri, 26 Jun 2020 13:17:35: end of X-cor INFO @ Fri, 26 Jun 2020 13:17:35: #2 finished! INFO @ Fri, 26 Jun 2020 13:17:35: #2 predicted fragment length is 169 bps INFO @ Fri, 26 Jun 2020 13:17:35: #2 alternative fragment length(s) may be 169 bps INFO @ Fri, 26 Jun 2020 13:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.20_model.r WARNING @ Fri, 26 Jun 2020 13:17:35: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 13:17:35: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Fri, 26 Jun 2020 13:17:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 13:17:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 13:17:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 13:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.10_peaks.xls INFO @ Fri, 26 Jun 2020 13:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 13:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.10_summits.bed INFO @ Fri, 26 Jun 2020 13:17:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8262 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 13:17:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 13:18:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.20_peaks.xls INFO @ Fri, 26 Jun 2020 13:18:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 13:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056722/SRX1056722.20_summits.bed INFO @ Fri, 26 Jun 2020 13:18:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5429 records, 4 fields): 8 millis CompletedMACS2peakCalling