Job ID = 6458875 SRX = SRX5717044 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:32 prefetch.2.10.7: 1) Downloading 'SRR8936405'... 2020-06-21T12:41:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:45:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:45:38 prefetch.2.10.7: 1) 'SRR8936405' was downloaded successfully Read 24468054 spots for SRR8936405/SRR8936405.sra Written 24468054 spots for SRR8936405/SRR8936405.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: 00:06:04 24468054 reads; of these: 24468054 (100.00%) were unpaired; of these: 2122564 (8.67%) aligned 0 times 17312041 (70.75%) aligned exactly 1 time 5033449 (20.57%) aligned >1 times 91.33% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 6681414 / 22345490 = 0.2990 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 21:57:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.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 21:57:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:31: 1000000 INFO @ Sun, 21 Jun 2020 21:57:37: 2000000 INFO @ Sun, 21 Jun 2020 21:57:44: 3000000 INFO @ Sun, 21 Jun 2020 21:57:50: 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 @ Sun, 21 Jun 2020 21:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.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 21:57:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:57: 5000000 INFO @ Sun, 21 Jun 2020 21:58:01: 1000000 INFO @ Sun, 21 Jun 2020 21:58:04: 6000000 INFO @ Sun, 21 Jun 2020 21:58:07: 2000000 INFO @ Sun, 21 Jun 2020 21:58:12: 7000000 INFO @ Sun, 21 Jun 2020 21:58:14: 3000000 INFO @ Sun, 21 Jun 2020 21:58:19: 8000000 INFO @ Sun, 21 Jun 2020 21:58:21: 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 @ Sun, 21 Jun 2020 21:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.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 21:58:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:26: 9000000 INFO @ Sun, 21 Jun 2020 21:58:27: 5000000 INFO @ Sun, 21 Jun 2020 21:58:31: 1000000 INFO @ Sun, 21 Jun 2020 21:58:33: 10000000 INFO @ Sun, 21 Jun 2020 21:58:34: 6000000 INFO @ Sun, 21 Jun 2020 21:58:39: 2000000 INFO @ Sun, 21 Jun 2020 21:58:41: 11000000 INFO @ Sun, 21 Jun 2020 21:58:41: 7000000 INFO @ Sun, 21 Jun 2020 21:58:46: 3000000 INFO @ Sun, 21 Jun 2020 21:58:48: 8000000 INFO @ Sun, 21 Jun 2020 21:58:48: 12000000 INFO @ Sun, 21 Jun 2020 21:58:54: 4000000 INFO @ Sun, 21 Jun 2020 21:58:54: 9000000 INFO @ Sun, 21 Jun 2020 21:58:56: 13000000 INFO @ Sun, 21 Jun 2020 21:59:01: 10000000 INFO @ Sun, 21 Jun 2020 21:59:01: 5000000 INFO @ Sun, 21 Jun 2020 21:59:03: 14000000 INFO @ Sun, 21 Jun 2020 21:59:08: 11000000 INFO @ Sun, 21 Jun 2020 21:59:09: 6000000 INFO @ Sun, 21 Jun 2020 21:59:10: 15000000 INFO @ Sun, 21 Jun 2020 21:59:15: 12000000 INFO @ Sun, 21 Jun 2020 21:59:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:59:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:59:16: #1 total tags in treatment: 15664076 INFO @ Sun, 21 Jun 2020 21:59:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:16: #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 21:59:16: #1 tags after filtering in treatment: 15663984 INFO @ Sun, 21 Jun 2020 21:59:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:16: 7000000 INFO @ Sun, 21 Jun 2020 21:59:17: #2 number of paired peaks: 193 WARNING @ Sun, 21 Jun 2020 21:59:17: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:17: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 21:59:17: #2 alternative fragment length(s) may be 25,47,65,81,105,133,224,245,404,450,478,511,531,564 bps INFO @ Sun, 21 Jun 2020 21:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.05_model.r WARNING @ Sun, 21 Jun 2020 21:59:17: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:17: #2 You may need to consider one of the other alternative d(s): 25,47,65,81,105,133,224,245,404,450,478,511,531,564 WARNING @ Sun, 21 Jun 2020 21:59:17: #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 21:59:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:22: 13000000 INFO @ Sun, 21 Jun 2020 21:59:24: 8000000 INFO @ Sun, 21 Jun 2020 21:59:29: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:59:31: 9000000 INFO @ Sun, 21 Jun 2020 21:59:36: 15000000 INFO @ Sun, 21 Jun 2020 21:59:39: 10000000 INFO @ Sun, 21 Jun 2020 21:59:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:59:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:59:41: #1 total tags in treatment: 15664076 INFO @ Sun, 21 Jun 2020 21:59:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:41: #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 21:59:41: #1 tags after filtering in treatment: 15663984 INFO @ Sun, 21 Jun 2020 21:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:42: #2 number of paired peaks: 193 WARNING @ Sun, 21 Jun 2020 21:59:42: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:42: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 21:59:42: #2 alternative fragment length(s) may be 25,47,65,81,105,133,224,245,404,450,478,511,531,564 bps INFO @ Sun, 21 Jun 2020 21:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.10_model.r WARNING @ Sun, 21 Jun 2020 21:59:42: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:42: #2 You may need to consider one of the other alternative d(s): 25,47,65,81,105,133,224,245,404,450,478,511,531,564 WARNING @ Sun, 21 Jun 2020 21:59:42: #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 21:59:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:46: 11000000 INFO @ Sun, 21 Jun 2020 21:59:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:52: 12000000 INFO @ Sun, 21 Jun 2020 21:59:59: 13000000 INFO @ Sun, 21 Jun 2020 22:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:01: Done! pass1 - making usageList (450 chroms): 1 millis pass2 - checking and writing primary data (1851 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:00:06: 14000000 INFO @ Sun, 21 Jun 2020 22:00:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:13: 15000000 INFO @ Sun, 21 Jun 2020 22:00:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:00:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:00:18: #1 total tags in treatment: 15664076 INFO @ Sun, 21 Jun 2020 22:00:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:18: #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 22:00:18: #1 tags after filtering in treatment: 15663984 INFO @ Sun, 21 Jun 2020 22:00:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:19: #2 number of paired peaks: 193 WARNING @ Sun, 21 Jun 2020 22:00:19: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:19: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 22:00:19: #2 alternative fragment length(s) may be 25,47,65,81,105,133,224,245,404,450,478,511,531,564 bps INFO @ Sun, 21 Jun 2020 22:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.20_model.r WARNING @ Sun, 21 Jun 2020 22:00:19: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:19: #2 You may need to consider one of the other alternative d(s): 25,47,65,81,105,133,224,245,404,450,478,511,531,564 WARNING @ Sun, 21 Jun 2020 22:00:19: #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 22:00:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:26: Done! pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717044/SRX5717044.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:02: Done! pass1 - making usageList (50 chroms): 0 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling