Job ID = 6509143 SRX = SRX685465 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:13:58 prefetch.2.10.7: 1) Downloading 'SRR1556387'... 2020-06-26T15:13:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:18:59 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:18:59 prefetch.2.10.7: 1) 'SRR1556387' was downloaded successfully Read 47249812 spots for SRR1556387/SRR1556387.sra Written 47249812 spots for SRR1556387/SRR1556387.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: 00:15:26 47249812 reads; of these: 47249812 (100.00%) were unpaired; of these: 1967607 (4.16%) aligned 0 times 28327208 (59.95%) aligned exactly 1 time 16954997 (35.88%) aligned >1 times 95.84% overall alignment rate Time searching: 00:15:26 Overall time: 00:15:26 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 20 files... [bam_rmdupse_core] 12842245 / 45282205 = 0.2836 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 @ Sat, 27 Jun 2020 00:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.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 @ Sat, 27 Jun 2020 00:46:41: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:46:41: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:46:46: 1000000 INFO @ Sat, 27 Jun 2020 00:46:52: 2000000 INFO @ Sat, 27 Jun 2020 00:46:57: 3000000 INFO @ Sat, 27 Jun 2020 00:47:03: 4000000 INFO @ Sat, 27 Jun 2020 00:47:08: 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 @ Sat, 27 Jun 2020 00:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.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 @ Sat, 27 Jun 2020 00:47:10: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:47:10: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:47:14: 6000000 INFO @ Sat, 27 Jun 2020 00:47:17: 1000000 INFO @ Sat, 27 Jun 2020 00:47:20: 7000000 INFO @ Sat, 27 Jun 2020 00:47:24: 2000000 INFO @ Sat, 27 Jun 2020 00:47:26: 8000000 INFO @ Sat, 27 Jun 2020 00:47:31: 3000000 INFO @ Sat, 27 Jun 2020 00:47:33: 9000000 INFO @ Sat, 27 Jun 2020 00:47:38: 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 @ Sat, 27 Jun 2020 00:47:39: 10000000 INFO @ Sat, 27 Jun 2020 00:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.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 @ Sat, 27 Jun 2020 00:47:40: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:47:40: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:47:45: 11000000 INFO @ Sat, 27 Jun 2020 00:47:45: 5000000 INFO @ Sat, 27 Jun 2020 00:47:47: 1000000 INFO @ Sat, 27 Jun 2020 00:47:51: 12000000 INFO @ Sat, 27 Jun 2020 00:47:52: 6000000 INFO @ Sat, 27 Jun 2020 00:47:53: 2000000 INFO @ Sat, 27 Jun 2020 00:47:58: 13000000 INFO @ Sat, 27 Jun 2020 00:47:59: 7000000 INFO @ Sat, 27 Jun 2020 00:47:59: 3000000 INFO @ Sat, 27 Jun 2020 00:48:04: 14000000 INFO @ Sat, 27 Jun 2020 00:48:06: 4000000 INFO @ Sat, 27 Jun 2020 00:48:06: 8000000 INFO @ Sat, 27 Jun 2020 00:48:10: 15000000 INFO @ Sat, 27 Jun 2020 00:48:12: 5000000 INFO @ Sat, 27 Jun 2020 00:48:13: 9000000 INFO @ Sat, 27 Jun 2020 00:48:17: 16000000 INFO @ Sat, 27 Jun 2020 00:48:18: 6000000 INFO @ Sat, 27 Jun 2020 00:48:20: 10000000 INFO @ Sat, 27 Jun 2020 00:48:23: 17000000 INFO @ Sat, 27 Jun 2020 00:48:24: 7000000 INFO @ Sat, 27 Jun 2020 00:48:27: 11000000 INFO @ Sat, 27 Jun 2020 00:48:29: 18000000 INFO @ Sat, 27 Jun 2020 00:48:30: 8000000 INFO @ Sat, 27 Jun 2020 00:48:34: 12000000 INFO @ Sat, 27 Jun 2020 00:48:36: 19000000 INFO @ Sat, 27 Jun 2020 00:48:37: 9000000 INFO @ Sat, 27 Jun 2020 00:48:41: 13000000 INFO @ Sat, 27 Jun 2020 00:48:42: 20000000 INFO @ Sat, 27 Jun 2020 00:48:43: 10000000 INFO @ Sat, 27 Jun 2020 00:48:48: 14000000 INFO @ Sat, 27 Jun 2020 00:48:48: 21000000 INFO @ Sat, 27 Jun 2020 00:48:49: 11000000 INFO @ Sat, 27 Jun 2020 00:48:55: 15000000 INFO @ Sat, 27 Jun 2020 00:48:55: 22000000 INFO @ Sat, 27 Jun 2020 00:48:56: 12000000 INFO @ Sat, 27 Jun 2020 00:49:01: 23000000 INFO @ Sat, 27 Jun 2020 00:49:01: 16000000 INFO @ Sat, 27 Jun 2020 00:49:02: 13000000 INFO @ Sat, 27 Jun 2020 00:49:07: 24000000 INFO @ Sat, 27 Jun 2020 00:49:08: 14000000 INFO @ Sat, 27 Jun 2020 00:49:08: 17000000 INFO @ Sat, 27 Jun 2020 00:49:14: 25000000 INFO @ Sat, 27 Jun 2020 00:49:15: 15000000 INFO @ Sat, 27 Jun 2020 00:49:15: 18000000 INFO @ Sat, 27 Jun 2020 00:49:20: 26000000 INFO @ Sat, 27 Jun 2020 00:49:21: 16000000 INFO @ Sat, 27 Jun 2020 00:49:22: 19000000 INFO @ Sat, 27 Jun 2020 00:49:26: 27000000 INFO @ Sat, 27 Jun 2020 00:49:27: 17000000 INFO @ Sat, 27 Jun 2020 00:49:29: 20000000 INFO @ Sat, 27 Jun 2020 00:49:33: 28000000 INFO @ Sat, 27 Jun 2020 00:49:34: 18000000 INFO @ Sat, 27 Jun 2020 00:49:36: 21000000 INFO @ Sat, 27 Jun 2020 00:49:39: 29000000 INFO @ Sat, 27 Jun 2020 00:49:40: 19000000 INFO @ Sat, 27 Jun 2020 00:49:43: 22000000 INFO @ Sat, 27 Jun 2020 00:49:46: 30000000 INFO @ Sat, 27 Jun 2020 00:49:46: 20000000 INFO @ Sat, 27 Jun 2020 00:49:50: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:49:52: 31000000 INFO @ Sat, 27 Jun 2020 00:49:53: 21000000 INFO @ Sat, 27 Jun 2020 00:49:57: 24000000 INFO @ Sat, 27 Jun 2020 00:49:58: 32000000 INFO @ Sat, 27 Jun 2020 00:49:59: 22000000 INFO @ Sat, 27 Jun 2020 00:50:01: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:50:01: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:50:01: #1 total tags in treatment: 32439960 INFO @ Sat, 27 Jun 2020 00:50:01: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:50:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:50:02: #1 tags after filtering in treatment: 32439901 INFO @ Sat, 27 Jun 2020 00:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:50:02: #1 finished! INFO @ Sat, 27 Jun 2020 00:50:02: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:50:04: 25000000 INFO @ Sat, 27 Jun 2020 00:50:04: #2 number of paired peaks: 1123 INFO @ Sat, 27 Jun 2020 00:50:04: start model_add_line... INFO @ Sat, 27 Jun 2020 00:50:04: start X-correlation... INFO @ Sat, 27 Jun 2020 00:50:04: end of X-cor INFO @ Sat, 27 Jun 2020 00:50:04: #2 finished! INFO @ Sat, 27 Jun 2020 00:50:04: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:50:04: #2 alternative fragment length(s) may be 1,23,44 bps INFO @ Sat, 27 Jun 2020 00:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.05_model.r WARNING @ Sat, 27 Jun 2020 00:50:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:50:04: #2 You may need to consider one of the other alternative d(s): 1,23,44 WARNING @ Sat, 27 Jun 2020 00:50:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:50:04: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:50:05: 23000000 INFO @ Sat, 27 Jun 2020 00:50:10: 26000000 INFO @ Sat, 27 Jun 2020 00:50:11: 24000000 INFO @ Sat, 27 Jun 2020 00:50:17: 27000000 INFO @ Sat, 27 Jun 2020 00:50:17: 25000000 INFO @ Sat, 27 Jun 2020 00:50:23: 26000000 INFO @ Sat, 27 Jun 2020 00:50:24: 28000000 INFO @ Sat, 27 Jun 2020 00:50:30: 27000000 INFO @ Sat, 27 Jun 2020 00:50:31: 29000000 INFO @ Sat, 27 Jun 2020 00:50:36: 28000000 INFO @ Sat, 27 Jun 2020 00:50:38: 30000000 INFO @ Sat, 27 Jun 2020 00:50:42: 29000000 INFO @ Sat, 27 Jun 2020 00:50:45: 31000000 INFO @ Sat, 27 Jun 2020 00:50:49: 30000000 INFO @ Sat, 27 Jun 2020 00:50:52: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:50:52: 32000000 INFO @ Sat, 27 Jun 2020 00:50:55: 31000000 INFO @ Sat, 27 Jun 2020 00:50:55: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:50:55: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:50:55: #1 total tags in treatment: 32439960 INFO @ Sat, 27 Jun 2020 00:50:55: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:50:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:50:56: #1 tags after filtering in treatment: 32439901 INFO @ Sat, 27 Jun 2020 00:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:50:56: #1 finished! INFO @ Sat, 27 Jun 2020 00:50:56: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:50:58: #2 number of paired peaks: 1123 INFO @ Sat, 27 Jun 2020 00:50:58: start model_add_line... INFO @ Sat, 27 Jun 2020 00:50:58: start X-correlation... INFO @ Sat, 27 Jun 2020 00:50:58: end of X-cor INFO @ Sat, 27 Jun 2020 00:50:58: #2 finished! INFO @ Sat, 27 Jun 2020 00:50:58: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:50:58: #2 alternative fragment length(s) may be 1,23,44 bps INFO @ Sat, 27 Jun 2020 00:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.10_model.r WARNING @ Sat, 27 Jun 2020 00:50:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:50:58: #2 You may need to consider one of the other alternative d(s): 1,23,44 WARNING @ Sat, 27 Jun 2020 00:50:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:50:58: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:51:01: 32000000 INFO @ Sat, 27 Jun 2020 00:51:03: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:51:03: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:51:03: #1 total tags in treatment: 32439960 INFO @ Sat, 27 Jun 2020 00:51:03: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:51:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:51:04: #1 tags after filtering in treatment: 32439901 INFO @ Sat, 27 Jun 2020 00:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:51:04: #1 finished! INFO @ Sat, 27 Jun 2020 00:51:04: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:51:06: #2 number of paired peaks: 1123 INFO @ Sat, 27 Jun 2020 00:51:06: start model_add_line... INFO @ Sat, 27 Jun 2020 00:51:06: start X-correlation... INFO @ Sat, 27 Jun 2020 00:51:06: end of X-cor INFO @ Sat, 27 Jun 2020 00:51:06: #2 finished! INFO @ Sat, 27 Jun 2020 00:51:06: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:51:06: #2 alternative fragment length(s) may be 1,23,44 bps INFO @ Sat, 27 Jun 2020 00:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.20_model.r WARNING @ Sat, 27 Jun 2020 00:51:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:51:06: #2 You may need to consider one of the other alternative d(s): 1,23,44 WARNING @ Sat, 27 Jun 2020 00:51:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:51:06: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.05_summits.bed INFO @ Sat, 27 Jun 2020 00:51:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:51:45: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:51:52: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.10_summits.bed INFO @ Sat, 27 Jun 2020 00:52:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685465/SRX685465.20_summits.bed INFO @ Sat, 27 Jun 2020 00:52:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling