Job ID = 6456287 SRX = SRX335492 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:03:31 prefetch.2.10.7: 1) Downloading 'SRR952834'... 2020-06-21T11:03:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:42 prefetch.2.10.7: 1) 'SRR952834' was downloaded successfully Read 29099060 spots for SRR952834/SRR952834.sra Written 29099060 spots for SRR952834/SRR952834.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: 00:05:14 29099060 reads; of these: 29099060 (100.00%) were unpaired; of these: 15090366 (51.86%) aligned 0 times 11251091 (38.66%) aligned exactly 1 time 2757603 (9.48%) aligned >1 times 48.14% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 3634098 / 14008694 = 0.2594 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 20:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.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 20:18:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:19: 1000000 INFO @ Sun, 21 Jun 2020 20:18:26: 2000000 INFO @ Sun, 21 Jun 2020 20:18:33: 3000000 INFO @ Sun, 21 Jun 2020 20:18:40: 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 20:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.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 20:18:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:47: 5000000 INFO @ Sun, 21 Jun 2020 20:18:49: 1000000 INFO @ Sun, 21 Jun 2020 20:18:55: 6000000 INFO @ Sun, 21 Jun 2020 20:18:56: 2000000 INFO @ Sun, 21 Jun 2020 20:19:03: 7000000 INFO @ Sun, 21 Jun 2020 20:19:04: 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 @ Sun, 21 Jun 2020 20:19:10: 8000000 INFO @ Sun, 21 Jun 2020 20:19:11: 4000000 INFO @ Sun, 21 Jun 2020 20:19:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.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 20:19:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:18: 9000000 INFO @ Sun, 21 Jun 2020 20:19:18: 5000000 INFO @ Sun, 21 Jun 2020 20:19:19: 1000000 INFO @ Sun, 21 Jun 2020 20:19:26: 2000000 INFO @ Sun, 21 Jun 2020 20:19:26: 6000000 INFO @ Sun, 21 Jun 2020 20:19:26: 10000000 INFO @ Sun, 21 Jun 2020 20:19:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:19:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:19:30: #1 total tags in treatment: 10374596 INFO @ Sun, 21 Jun 2020 20:19:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:30: #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 20:19:30: #1 tags after filtering in treatment: 10374569 INFO @ Sun, 21 Jun 2020 20:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:31: #2 number of paired peaks: 347 WARNING @ Sun, 21 Jun 2020 20:19:31: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sun, 21 Jun 2020 20:19:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:31: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:19:31: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 20:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.05_model.r WARNING @ Sun, 21 Jun 2020 20:19:31: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:19:31: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 20:19:31: #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 20:19:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:33: 3000000 INFO @ Sun, 21 Jun 2020 20:19:34: 7000000 INFO @ Sun, 21 Jun 2020 20:19:40: 4000000 INFO @ Sun, 21 Jun 2020 20:19:41: 8000000 INFO @ Sun, 21 Jun 2020 20:19:47: 5000000 INFO @ Sun, 21 Jun 2020 20:19:49: 9000000 INFO @ Sun, 21 Jun 2020 20:19:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:54: 6000000 INFO @ Sun, 21 Jun 2020 20:19:57: 10000000 INFO @ Sun, 21 Jun 2020 20:20:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:00: #1 total tags in treatment: 10374596 INFO @ Sun, 21 Jun 2020 20:20:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:00: #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 20:20:01: #1 tags after filtering in treatment: 10374569 INFO @ Sun, 21 Jun 2020 20:20:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:01: 7000000 INFO @ Sun, 21 Jun 2020 20:20:01: #2 number of paired peaks: 347 WARNING @ Sun, 21 Jun 2020 20:20:01: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sun, 21 Jun 2020 20:20:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:02: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:20:02: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 20:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.10_model.r WARNING @ Sun, 21 Jun 2020 20:20:02: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:20:02: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 20:20:02: #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 20:20:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.05_summits.bed INFO @ Sun, 21 Jun 2020 20:20:05: Done! pass1 - making usageList (430 chroms): 2 millis pass2 - checking and writing primary data (2367 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:20:07: 8000000 INFO @ Sun, 21 Jun 2020 20:20:14: 9000000 INFO @ Sun, 21 Jun 2020 20:20:21: 10000000 INFO @ Sun, 21 Jun 2020 20:20:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:24: #1 total tags in treatment: 10374596 INFO @ Sun, 21 Jun 2020 20:20:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:24: #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 20:20:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:24: #1 tags after filtering in treatment: 10374569 INFO @ Sun, 21 Jun 2020 20:20:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:25: #2 number of paired peaks: 347 WARNING @ Sun, 21 Jun 2020 20:20:25: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sun, 21 Jun 2020 20:20:25: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:25: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:25: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:25: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:25: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:20:25: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 20:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.20_model.r WARNING @ Sun, 21 Jun 2020 20:20:25: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:20:25: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 20:20:25: #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 20:20:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.10_summits.bed INFO @ Sun, 21 Jun 2020 20:20:35: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (1428 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:20:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335492/SRX335492.20_summits.bed INFO @ Sun, 21 Jun 2020 20:21:00: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 5 millis CompletedMACS2peakCalling