Job ID = 6627308 SRX = SRX8521365 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:56:39 prefetch.2.10.7: 1) Downloading 'SRR11978126'... 2020-07-14T01:56:39 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:57:59 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:57:59 prefetch.2.10.7: 'SRR11978126' is valid 2020-07-14T01:57:59 prefetch.2.10.7: 1) 'SRR11978126' was downloaded successfully 2020-07-14T01:57:59 prefetch.2.10.7: 'SRR11978126' has 0 unresolved dependencies Read 10605348 spots for SRR11978126/SRR11978126.sra Written 10605348 spots for SRR11978126/SRR11978126.sra 2020-07-14T01:58:48 prefetch.2.10.7: 1) Downloading 'SRR11978127'... 2020-07-14T01:58:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:00:15 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:00:16 prefetch.2.10.7: 'SRR11978127' is valid 2020-07-14T02:00:16 prefetch.2.10.7: 1) 'SRR11978127' was downloaded successfully 2020-07-14T02:00:16 prefetch.2.10.7: 'SRR11978127' has 0 unresolved dependencies Read 10479259 spots for SRR11978127/SRR11978127.sra Written 10479259 spots for SRR11978127/SRR11978127.sra 2020-07-14T02:01:05 prefetch.2.10.7: 1) Downloading 'SRR11978128'... 2020-07-14T02:01:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:27 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:28 prefetch.2.10.7: 'SRR11978128' is valid 2020-07-14T02:02:28 prefetch.2.10.7: 1) 'SRR11978128' was downloaded successfully 2020-07-14T02:02:28 prefetch.2.10.7: 'SRR11978128' has 0 unresolved dependencies Read 10842086 spots for SRR11978128/SRR11978128.sra Written 10842086 spots for SRR11978128/SRR11978128.sra 2020-07-14T02:03:21 prefetch.2.10.7: 1) Downloading 'SRR11978129'... 2020-07-14T02:03:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:04:54 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:04:54 prefetch.2.10.7: 'SRR11978129' is valid 2020-07-14T02:04:54 prefetch.2.10.7: 1) 'SRR11978129' was downloaded successfully 2020-07-14T02:04:54 prefetch.2.10.7: 'SRR11978129' has 0 unresolved dependencies Read 10881805 spots for SRR11978129/SRR11978129.sra Written 10881805 spots for SRR11978129/SRR11978129.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627532 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:34 42808498 reads; of these: 42808498 (100.00%) were unpaired; of these: 34248001 (80.00%) aligned 0 times 6323787 (14.77%) aligned exactly 1 time 2236710 (5.22%) aligned >1 times 20.00% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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_rmdupse_core] 1478707 / 8560497 = 0.1727 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 @ Tue, 14 Jul 2020 11:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.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 @ Tue, 14 Jul 2020 11:16:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:12: 1000000 INFO @ Tue, 14 Jul 2020 11:16:18: 2000000 INFO @ Tue, 14 Jul 2020 11:16:24: 3000000 INFO @ Tue, 14 Jul 2020 11:16:29: 4000000 INFO @ Tue, 14 Jul 2020 11:16:35: 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 @ Tue, 14 Jul 2020 11:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.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 @ Tue, 14 Jul 2020 11:16:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:41: 6000000 INFO @ Tue, 14 Jul 2020 11:16:43: 1000000 INFO @ Tue, 14 Jul 2020 11:16:47: 7000000 INFO @ Tue, 14 Jul 2020 11:16:47: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:16:47: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:16:47: #1 total tags in treatment: 7081790 INFO @ Tue, 14 Jul 2020 11:16:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:16:47: #1 tags after filtering in treatment: 7081790 INFO @ Tue, 14 Jul 2020 11:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:16:47: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:48: #2 number of paired peaks: 287 WARNING @ Tue, 14 Jul 2020 11:16:48: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 14 Jul 2020 11:16:48: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:48: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:48: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:48: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:48: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:16:48: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.05_model.r WARNING @ Tue, 14 Jul 2020 11:16:48: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:16:48: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:16:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:16:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:16:49: 2000000 INFO @ Tue, 14 Jul 2020 11:16:55: 3000000 INFO @ Tue, 14 Jul 2020 11:17:01: 4000000 INFO @ Tue, 14 Jul 2020 11:17:02: #3 Call peaks for each chromosome... 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 @ Tue, 14 Jul 2020 11:17:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.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 @ Tue, 14 Jul 2020 11:17:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:07: 5000000 INFO @ Tue, 14 Jul 2020 11:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.05_summits.bed INFO @ Tue, 14 Jul 2020 11:17:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1908 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:13: 1000000 INFO @ Tue, 14 Jul 2020 11:17:13: 6000000 INFO @ Tue, 14 Jul 2020 11:17:19: 2000000 INFO @ Tue, 14 Jul 2020 11:17:19: 7000000 INFO @ Tue, 14 Jul 2020 11:17:20: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:17:20: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:17:20: #1 total tags in treatment: 7081790 INFO @ Tue, 14 Jul 2020 11:17:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:17:20: #1 tags after filtering in treatment: 7081790 INFO @ Tue, 14 Jul 2020 11:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:20: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:21: #2 number of paired peaks: 287 WARNING @ Tue, 14 Jul 2020 11:17:21: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:21: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:21: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:21: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:21: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:21: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:17:21: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:17:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.10_model.r WARNING @ Tue, 14 Jul 2020 11:17:21: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:17:21: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:17:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:17:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:25: 3000000 INFO @ Tue, 14 Jul 2020 11:17:31: 4000000 INFO @ Tue, 14 Jul 2020 11:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:37: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.10_summits.bed INFO @ Tue, 14 Jul 2020 11:17:42: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (832 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:43: 6000000 INFO @ Tue, 14 Jul 2020 11:17:49: 7000000 INFO @ Tue, 14 Jul 2020 11:17:50: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:17:50: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:17:50: #1 total tags in treatment: 7081790 INFO @ Tue, 14 Jul 2020 11:17:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:17:50: #1 tags after filtering in treatment: 7081790 INFO @ Tue, 14 Jul 2020 11:17:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:50: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:50: #2 number of paired peaks: 287 WARNING @ Tue, 14 Jul 2020 11:17:50: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:50: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:50: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:50: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:50: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:50: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:17:50: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.20_model.r WARNING @ Tue, 14 Jul 2020 11:17:50: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:17:50: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:17:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:17:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:18:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521365/SRX8521365.20_summits.bed INFO @ Tue, 14 Jul 2020 11:18:12: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 1 millis CompletedMACS2peakCalling