Job ID = 6453587 SRX = SRX128302 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:02 prefetch.2.10.7: 1) Downloading 'SRR442241'... 2020-06-21T08:40:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:45:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:45:46 prefetch.2.10.7: 1) 'SRR442241' was downloaded successfully Read 32430309 spots for SRR442241/SRR442241.sra Written 32430309 spots for SRR442241/SRR442241.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: 00:06:44 32430309 reads; of these: 32430309 (100.00%) were unpaired; of these: 4804834 (14.82%) aligned 0 times 19624490 (60.51%) aligned exactly 1 time 8000985 (24.67%) aligned >1 times 85.18% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 17418082 / 27625475 = 0.6305 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 18:00:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.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 18:00:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:23: 1000000 INFO @ Sun, 21 Jun 2020 18:00:28: 2000000 INFO @ Sun, 21 Jun 2020 18:00:34: 3000000 INFO @ Sun, 21 Jun 2020 18:00:39: 4000000 INFO @ Sun, 21 Jun 2020 18:00:44: 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 18:00:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.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 18:00:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:50: 6000000 INFO @ Sun, 21 Jun 2020 18:00:53: 1000000 INFO @ Sun, 21 Jun 2020 18:00:56: 7000000 INFO @ Sun, 21 Jun 2020 18:00:58: 2000000 INFO @ Sun, 21 Jun 2020 18:01:02: 8000000 INFO @ Sun, 21 Jun 2020 18:01:04: 3000000 INFO @ Sun, 21 Jun 2020 18:01:08: 9000000 INFO @ Sun, 21 Jun 2020 18:01:09: 4000000 INFO @ Sun, 21 Jun 2020 18:01:14: 10000000 INFO @ Sun, 21 Jun 2020 18:01:15: 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 18:01:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:01:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:01:16: #1 total tags in treatment: 10207393 INFO @ Sun, 21 Jun 2020 18:01:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:16: #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 18:01:17: #1 tags after filtering in treatment: 10207335 INFO @ Sun, 21 Jun 2020 18:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.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 18:01:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:18: #2 number of paired peaks: 3926 INFO @ Sun, 21 Jun 2020 18:01:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:18: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:01:18: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 18:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.05_model.r WARNING @ Sun, 21 Jun 2020 18:01:18: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:18: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 18:01:18: #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 18:01:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:21: 6000000 INFO @ Sun, 21 Jun 2020 18:01:23: 1000000 INFO @ Sun, 21 Jun 2020 18:01:26: 7000000 INFO @ Sun, 21 Jun 2020 18:01:29: 2000000 INFO @ Sun, 21 Jun 2020 18:01:32: 8000000 INFO @ Sun, 21 Jun 2020 18:01:34: 3000000 INFO @ Sun, 21 Jun 2020 18:01:38: 9000000 INFO @ Sun, 21 Jun 2020 18:01:40: 4000000 INFO @ Sun, 21 Jun 2020 18:01:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:44: 10000000 INFO @ Sun, 21 Jun 2020 18:01:45: 5000000 INFO @ Sun, 21 Jun 2020 18:01:46: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:01:46: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:01:46: #1 total tags in treatment: 10207393 INFO @ Sun, 21 Jun 2020 18:01:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:46: #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 18:01:46: #1 tags after filtering in treatment: 10207335 INFO @ Sun, 21 Jun 2020 18:01:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:47: #2 number of paired peaks: 3926 INFO @ Sun, 21 Jun 2020 18:01:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:47: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:01:47: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 18:01:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.10_model.r WARNING @ Sun, 21 Jun 2020 18:01:48: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:48: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 18:01:48: #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 18:01:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:51: 6000000 INFO @ Sun, 21 Jun 2020 18:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:51: Done! pass1 - making usageList (794 chroms): 3 millis pass2 - checking and writing primary data (11583 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:01:56: 7000000 INFO @ Sun, 21 Jun 2020 18:02:02: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:02:08: 9000000 INFO @ Sun, 21 Jun 2020 18:02:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:14: 10000000 INFO @ Sun, 21 Jun 2020 18:02:15: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:02:15: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:02:15: #1 total tags in treatment: 10207393 INFO @ Sun, 21 Jun 2020 18:02:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:15: #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 18:02:16: #1 tags after filtering in treatment: 10207335 INFO @ Sun, 21 Jun 2020 18:02:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:17: #2 number of paired peaks: 3926 INFO @ Sun, 21 Jun 2020 18:02:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:17: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:02:17: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 18:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.20_model.r WARNING @ Sun, 21 Jun 2020 18:02:17: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:17: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 18:02:17: #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 18:02:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.10_summits.bed INFO @ Sun, 21 Jun 2020 18:02:21: Done! pass1 - making usageList (696 chroms): 2 millis pass2 - checking and writing primary data (7080 records, 4 fields): 46 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128302/SRX128302.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:49: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (3463 records, 4 fields): 32 millis CompletedMACS2peakCalling