Job ID = 6452530 SRX = SRX016145 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:54:30 prefetch.2.10.7: 1) Downloading 'SRR034698'... 2020-06-21T07:54:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:56:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:56:19 prefetch.2.10.7: 'SRR034698' is valid 2020-06-21T07:56:19 prefetch.2.10.7: 1) 'SRR034698' was downloaded successfully Read 14232213 spots for SRR034698/SRR034698.sra Written 14232213 spots for SRR034698/SRR034698.sra 2020-06-21T07:57:05 prefetch.2.10.7: 1) Downloading 'SRR034699'... 2020-06-21T07:57:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:59:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:59:49 prefetch.2.10.7: 'SRR034699' is valid 2020-06-21T07:59:49 prefetch.2.10.7: 1) 'SRR034699' was downloaded successfully Read 12932448 spots for SRR034699/SRR034699.sra Written 12932448 spots for SRR034699/SRR034699.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: 00:05:04 27164661 reads; of these: 27164661 (100.00%) were unpaired; of these: 576243 (2.12%) aligned 0 times 22758663 (83.78%) aligned exactly 1 time 3829755 (14.10%) aligned >1 times 97.88% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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 8 files... [bam_rmdupse_core] 12341126 / 26588418 = 0.4642 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 17:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.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 17:10:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:10:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:03: 1000000 INFO @ Sun, 21 Jun 2020 17:11:08: 2000000 INFO @ Sun, 21 Jun 2020 17:11:13: 3000000 INFO @ Sun, 21 Jun 2020 17:11:18: 4000000 INFO @ Sun, 21 Jun 2020 17:11:23: 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 17:11:27: 6000000 INFO @ Sun, 21 Jun 2020 17:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.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 17:11:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:32: 7000000 INFO @ Sun, 21 Jun 2020 17:11:34: 1000000 INFO @ Sun, 21 Jun 2020 17:11:37: 8000000 INFO @ Sun, 21 Jun 2020 17:11:39: 2000000 INFO @ Sun, 21 Jun 2020 17:11:43: 9000000 INFO @ Sun, 21 Jun 2020 17:11:44: 3000000 INFO @ Sun, 21 Jun 2020 17:11:48: 10000000 INFO @ Sun, 21 Jun 2020 17:11:49: 4000000 INFO @ Sun, 21 Jun 2020 17:11:53: 11000000 INFO @ Sun, 21 Jun 2020 17:11:54: 5000000 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 17:11:58: 12000000 INFO @ Sun, 21 Jun 2020 17:11:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.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 17:11:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:59: 6000000 INFO @ Sun, 21 Jun 2020 17:12:03: 13000000 INFO @ Sun, 21 Jun 2020 17:12:04: 1000000 INFO @ Sun, 21 Jun 2020 17:12:04: 7000000 INFO @ Sun, 21 Jun 2020 17:12:09: 14000000 INFO @ Sun, 21 Jun 2020 17:12:09: 2000000 INFO @ Sun, 21 Jun 2020 17:12:09: 8000000 INFO @ Sun, 21 Jun 2020 17:12:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:12:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:12:10: #1 total tags in treatment: 14247292 INFO @ Sun, 21 Jun 2020 17:12:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:10: #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 17:12:10: #1 tags after filtering in treatment: 14247278 INFO @ Sun, 21 Jun 2020 17:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:11: #2 number of paired peaks: 524 WARNING @ Sun, 21 Jun 2020 17:12:11: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 21 Jun 2020 17:12:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:12: #2 predicted fragment length is 285 bps INFO @ Sun, 21 Jun 2020 17:12:12: #2 alternative fragment length(s) may be 285 bps INFO @ Sun, 21 Jun 2020 17:12:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.05_model.r INFO @ Sun, 21 Jun 2020 17:12:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:12:14: 9000000 INFO @ Sun, 21 Jun 2020 17:12:14: 3000000 INFO @ Sun, 21 Jun 2020 17:12:20: 4000000 INFO @ Sun, 21 Jun 2020 17:12:20: 10000000 INFO @ Sun, 21 Jun 2020 17:12:25: 5000000 INFO @ Sun, 21 Jun 2020 17:12:25: 11000000 INFO @ Sun, 21 Jun 2020 17:12:30: 6000000 INFO @ Sun, 21 Jun 2020 17:12:31: 12000000 INFO @ Sun, 21 Jun 2020 17:12:35: 7000000 INFO @ Sun, 21 Jun 2020 17:12:36: 13000000 INFO @ Sun, 21 Jun 2020 17:12:41: 8000000 INFO @ Sun, 21 Jun 2020 17:12:41: 14000000 INFO @ Sun, 21 Jun 2020 17:12:43: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:12:43: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:12:43: #1 total tags in treatment: 14247292 INFO @ Sun, 21 Jun 2020 17:12:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:43: #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 17:12:43: #1 tags after filtering in treatment: 14247278 INFO @ Sun, 21 Jun 2020 17:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:44: #2 number of paired peaks: 524 WARNING @ Sun, 21 Jun 2020 17:12:44: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 21 Jun 2020 17:12:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:44: #2 predicted fragment length is 285 bps INFO @ Sun, 21 Jun 2020 17:12:44: #2 alternative fragment length(s) may be 285 bps INFO @ Sun, 21 Jun 2020 17:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.10_model.r INFO @ Sun, 21 Jun 2020 17:12:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:12:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:12:46: 9000000 INFO @ Sun, 21 Jun 2020 17:12:51: 10000000 INFO @ Sun, 21 Jun 2020 17:12:56: 11000000 INFO @ Sun, 21 Jun 2020 17:13:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.05_summits.bed INFO @ Sun, 21 Jun 2020 17:13:01: Done! INFO @ Sun, 21 Jun 2020 17:13:01: 12000000 pass1 - making usageList (360 chroms): 2 millis pass2 - checking and writing primary data (6618 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:13:06: 13000000 INFO @ Sun, 21 Jun 2020 17:13:11: 14000000 INFO @ Sun, 21 Jun 2020 17:13:13: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:13:13: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:13:13: #1 total tags in treatment: 14247292 INFO @ Sun, 21 Jun 2020 17:13:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:13: #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 17:13:13: #1 tags after filtering in treatment: 14247278 INFO @ Sun, 21 Jun 2020 17:13:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:13: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:13:14: #2 number of paired peaks: 524 WARNING @ Sun, 21 Jun 2020 17:13:14: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 21 Jun 2020 17:13:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:14: #2 predicted fragment length is 285 bps INFO @ Sun, 21 Jun 2020 17:13:14: #2 alternative fragment length(s) may be 285 bps INFO @ Sun, 21 Jun 2020 17:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.20_model.r INFO @ Sun, 21 Jun 2020 17:13:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.10_summits.bed INFO @ Sun, 21 Jun 2020 17:13:33: Done! pass1 - making usageList (237 chroms): 1 millis pass2 - checking and writing primary data (2988 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016145/SRX016145.20_summits.bed INFO @ Sun, 21 Jun 2020 17:14:06: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (1159 records, 4 fields): 6 millis CompletedMACS2peakCalling