Job ID = 6498685 SRX = SRX699110 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:54:59 prefetch.2.10.7: 1) Downloading 'SRR1573151'... 2020-06-25T23:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:58:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:58:31 prefetch.2.10.7: 1) 'SRR1573151' was downloaded successfully Read 7060425 spots for SRR1573151/SRR1573151.sra Written 7060425 spots for SRR1573151/SRR1573151.sra 2020-06-25T23:59:26 prefetch.2.10.7: 1) Downloading 'SRR1573152'... 2020-06-25T23:59:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:48 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:48 prefetch.2.10.7: 1) 'SRR1573152' was downloaded successfully Read 7142051 spots for SRR1573152/SRR1573152.sra Written 7142051 spots for SRR1573152/SRR1573152.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: 00:00:01 Multiseed full-index search: 00:34:01 14202476 reads; of these: 14202476 (100.00%) were paired; of these: 1015242 (7.15%) aligned concordantly 0 times 10546945 (74.26%) aligned concordantly exactly 1 time 2640289 (18.59%) aligned concordantly >1 times ---- 1015242 pairs aligned concordantly 0 times; of these: 144008 (14.18%) aligned discordantly 1 time ---- 871234 pairs aligned 0 times concordantly or discordantly; of these: 1742468 mates make up the pairs; of these: 1043283 (59.87%) aligned 0 times 373993 (21.46%) aligned exactly 1 time 325192 (18.66%) aligned >1 times 96.33% overall alignment rate Time searching: 00:34:02 Overall time: 00:34:02 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_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] 2608995 / 13273307 = 0.1966 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 09:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.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 09:48:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:48:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:48:40: 1000000 INFO @ Fri, 26 Jun 2020 09:48:47: 2000000 INFO @ Fri, 26 Jun 2020 09:48:54: 3000000 INFO @ Fri, 26 Jun 2020 09:49:00: 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 09:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.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 09:49:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:49:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:49:08: 5000000 INFO @ Fri, 26 Jun 2020 09:49:13: 1000000 INFO @ Fri, 26 Jun 2020 09:49:16: 6000000 INFO @ Fri, 26 Jun 2020 09:49:22: 2000000 INFO @ Fri, 26 Jun 2020 09:49:25: 7000000 INFO @ Fri, 26 Jun 2020 09:49:31: 3000000 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 09:49:33: 8000000 INFO @ Fri, 26 Jun 2020 09:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.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 09:49:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:49:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:49:40: 4000000 INFO @ Fri, 26 Jun 2020 09:49:43: 1000000 INFO @ Fri, 26 Jun 2020 09:49:43: 9000000 INFO @ Fri, 26 Jun 2020 09:49:49: 5000000 INFO @ Fri, 26 Jun 2020 09:49:52: 10000000 INFO @ Fri, 26 Jun 2020 09:49:52: 2000000 INFO @ Fri, 26 Jun 2020 09:49:59: 6000000 INFO @ Fri, 26 Jun 2020 09:50:00: 11000000 INFO @ Fri, 26 Jun 2020 09:50:02: 3000000 INFO @ Fri, 26 Jun 2020 09:50:08: 7000000 INFO @ Fri, 26 Jun 2020 09:50:09: 12000000 INFO @ Fri, 26 Jun 2020 09:50:11: 4000000 INFO @ Fri, 26 Jun 2020 09:50:17: 8000000 INFO @ Fri, 26 Jun 2020 09:50:18: 13000000 INFO @ Fri, 26 Jun 2020 09:50:20: 5000000 INFO @ Fri, 26 Jun 2020 09:50:26: 9000000 INFO @ Fri, 26 Jun 2020 09:50:27: 14000000 INFO @ Fri, 26 Jun 2020 09:50:30: 6000000 INFO @ Fri, 26 Jun 2020 09:50:36: 10000000 INFO @ Fri, 26 Jun 2020 09:50:36: 15000000 INFO @ Fri, 26 Jun 2020 09:50:40: 7000000 INFO @ Fri, 26 Jun 2020 09:50:45: 16000000 INFO @ Fri, 26 Jun 2020 09:50:45: 11000000 INFO @ Fri, 26 Jun 2020 09:50:50: 8000000 INFO @ Fri, 26 Jun 2020 09:50:54: 17000000 INFO @ Fri, 26 Jun 2020 09:50:55: 12000000 INFO @ Fri, 26 Jun 2020 09:50:59: 9000000 INFO @ Fri, 26 Jun 2020 09:51:04: 18000000 INFO @ Fri, 26 Jun 2020 09:51:05: 13000000 INFO @ Fri, 26 Jun 2020 09:51:09: 10000000 INFO @ Fri, 26 Jun 2020 09:51:13: 19000000 INFO @ Fri, 26 Jun 2020 09:51:14: 14000000 INFO @ Fri, 26 Jun 2020 09:51:19: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:51:22: 20000000 INFO @ Fri, 26 Jun 2020 09:51:24: 15000000 INFO @ Fri, 26 Jun 2020 09:51:30: 12000000 INFO @ Fri, 26 Jun 2020 09:51:31: 21000000 INFO @ Fri, 26 Jun 2020 09:51:34: 16000000 INFO @ Fri, 26 Jun 2020 09:51:39: 13000000 INFO @ Fri, 26 Jun 2020 09:51:40: 22000000 INFO @ Fri, 26 Jun 2020 09:51:42: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:51:42: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:51:42: #1 total tags in treatment: 10596415 INFO @ Fri, 26 Jun 2020 09:51:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:51:42: #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 09:51:42: #1 tags after filtering in treatment: 9734674 INFO @ Fri, 26 Jun 2020 09:51:42: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:51:42: #1 finished! INFO @ Fri, 26 Jun 2020 09:51:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:51:42: #2 number of paired peaks: 964 WARNING @ Fri, 26 Jun 2020 09:51:42: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Fri, 26 Jun 2020 09:51:42: start model_add_line... INFO @ Fri, 26 Jun 2020 09:51:43: start X-correlation... INFO @ Fri, 26 Jun 2020 09:51:43: end of X-cor INFO @ Fri, 26 Jun 2020 09:51:43: #2 finished! INFO @ Fri, 26 Jun 2020 09:51:43: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 09:51:43: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 26 Jun 2020 09:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.05_model.r WARNING @ Fri, 26 Jun 2020 09:51:43: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:51:43: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Fri, 26 Jun 2020 09:51:43: #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 09:51:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:51:44: 17000000 INFO @ Fri, 26 Jun 2020 09:51:49: 14000000 INFO @ Fri, 26 Jun 2020 09:51:53: 18000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:51:59: 15000000 INFO @ Fri, 26 Jun 2020 09:52:03: 19000000 INFO @ Fri, 26 Jun 2020 09:52:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:52:09: 16000000 INFO @ Fri, 26 Jun 2020 09:52:13: 20000000 INFO @ Fri, 26 Jun 2020 09:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.05_summits.bed INFO @ Fri, 26 Jun 2020 09:52:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13190 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:52:19: 17000000 INFO @ Fri, 26 Jun 2020 09:52:22: 21000000 INFO @ Fri, 26 Jun 2020 09:52:29: 18000000 INFO @ Fri, 26 Jun 2020 09:52:32: 22000000 INFO @ Fri, 26 Jun 2020 09:52:33: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:52:33: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:52:33: #1 total tags in treatment: 10596415 INFO @ Fri, 26 Jun 2020 09:52:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:52:33: #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 09:52:33: #1 tags after filtering in treatment: 9734674 INFO @ Fri, 26 Jun 2020 09:52:33: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:52:33: #1 finished! INFO @ Fri, 26 Jun 2020 09:52:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:52:34: #2 number of paired peaks: 964 WARNING @ Fri, 26 Jun 2020 09:52:34: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Fri, 26 Jun 2020 09:52:34: start model_add_line... INFO @ Fri, 26 Jun 2020 09:52:34: start X-correlation... INFO @ Fri, 26 Jun 2020 09:52:34: end of X-cor INFO @ Fri, 26 Jun 2020 09:52:34: #2 finished! INFO @ Fri, 26 Jun 2020 09:52:34: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 09:52:34: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 26 Jun 2020 09:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.10_model.r WARNING @ Fri, 26 Jun 2020 09:52:34: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:52:34: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Fri, 26 Jun 2020 09:52:34: #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 09:52:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:52:38: 19000000 INFO @ Fri, 26 Jun 2020 09:52:47: 20000000 INFO @ Fri, 26 Jun 2020 09:52:56: 21000000 INFO @ Fri, 26 Jun 2020 09:52:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:53:04: 22000000 INFO @ Fri, 26 Jun 2020 09:53:06: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:53:06: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:53:06: #1 total tags in treatment: 10596415 INFO @ Fri, 26 Jun 2020 09:53:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:53:06: #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 09:53:06: #1 tags after filtering in treatment: 9734674 INFO @ Fri, 26 Jun 2020 09:53:06: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:53:06: #1 finished! INFO @ Fri, 26 Jun 2020 09:53:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:53:07: #2 number of paired peaks: 964 WARNING @ Fri, 26 Jun 2020 09:53:07: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Fri, 26 Jun 2020 09:53:07: start model_add_line... INFO @ Fri, 26 Jun 2020 09:53:07: start X-correlation... INFO @ Fri, 26 Jun 2020 09:53:07: end of X-cor INFO @ Fri, 26 Jun 2020 09:53:07: #2 finished! INFO @ Fri, 26 Jun 2020 09:53:07: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 09:53:07: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 26 Jun 2020 09:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.20_model.r WARNING @ Fri, 26 Jun 2020 09:53:07: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:53:07: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Fri, 26 Jun 2020 09:53:07: #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 09:53:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.10_summits.bed INFO @ Fri, 26 Jun 2020 09:53:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4589 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:53:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699110/SRX699110.20_summits.bed INFO @ Fri, 26 Jun 2020 09:53:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1263 records, 4 fields): 3 millis CompletedMACS2peakCalling