Job ID = 6453845 SRX = SRX152100 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:45:17 prefetch.2.10.7: 1) Downloading 'SRR504956'... 2020-06-21T08:45:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:49:04 prefetch.2.10.7: 1) 'SRR504956' was downloaded successfully Read 20241401 spots for SRR504956/SRR504956.sra Written 20241401 spots for SRR504956/SRR504956.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: 00:08:16 20241401 reads; of these: 20241401 (100.00%) were unpaired; of these: 7036014 (34.76%) aligned 0 times 4957686 (24.49%) aligned exactly 1 time 8247701 (40.75%) aligned >1 times 65.24% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 6659750 / 13205387 = 0.5043 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 18:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.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 18:01:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:44: 1000000 INFO @ Sun, 21 Jun 2020 18:01:50: 2000000 INFO @ Sun, 21 Jun 2020 18:01:56: 3000000 INFO @ Sun, 21 Jun 2020 18:02:02: 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 18:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.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 18:02:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:08: 5000000 INFO @ Sun, 21 Jun 2020 18:02:15: 6000000 INFO @ Sun, 21 Jun 2020 18:02:16: 1000000 INFO @ Sun, 21 Jun 2020 18:02:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:02:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:02:20: #1 total tags in treatment: 6545637 INFO @ Sun, 21 Jun 2020 18:02:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:20: #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 18:02:20: #1 tags after filtering in treatment: 6545620 INFO @ Sun, 21 Jun 2020 18:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:21: #2 number of paired peaks: 1952 INFO @ Sun, 21 Jun 2020 18:02:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:21: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:02:21: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 18:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.05_model.r WARNING @ Sun, 21 Jun 2020 18:02:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:21: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 18:02:21: #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 18:02:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:23: 2000000 INFO @ Sun, 21 Jun 2020 18:02:30: 3000000 INFO @ Sun, 21 Jun 2020 18:02:35: #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 @ Sun, 21 Jun 2020 18:02:37: 4000000 INFO @ Sun, 21 Jun 2020 18:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.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 18:02:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.05_summits.bed INFO @ Sun, 21 Jun 2020 18:02:42: Done! pass1 - making usageList (758 chroms): 1 millis pass2 - checking and writing primary data (5300 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:45: 5000000 INFO @ Sun, 21 Jun 2020 18:02:45: 1000000 INFO @ Sun, 21 Jun 2020 18:02:53: 2000000 INFO @ Sun, 21 Jun 2020 18:02:53: 6000000 INFO @ Sun, 21 Jun 2020 18:02:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:02:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:02:58: #1 total tags in treatment: 6545637 INFO @ Sun, 21 Jun 2020 18:02:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:58: #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 18:02:58: #1 tags after filtering in treatment: 6545620 INFO @ Sun, 21 Jun 2020 18:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:59: #2 number of paired peaks: 1952 INFO @ Sun, 21 Jun 2020 18:02:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:59: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:02:59: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 18:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.10_model.r WARNING @ Sun, 21 Jun 2020 18:02:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:59: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 18:02:59: #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 18:02:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:03:00: 3000000 INFO @ Sun, 21 Jun 2020 18:03:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:03:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:14: 5000000 INFO @ Sun, 21 Jun 2020 18:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.10_summits.bed INFO @ Sun, 21 Jun 2020 18:03:19: Done! INFO @ Sun, 21 Jun 2020 18:03:20: 6000000 pass1 - making usageList (621 chroms): 1 millis pass2 - checking and writing primary data (3704 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:03:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:03:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:03:23: #1 total tags in treatment: 6545637 INFO @ Sun, 21 Jun 2020 18:03:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:23: #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 18:03:23: #1 tags after filtering in treatment: 6545620 INFO @ Sun, 21 Jun 2020 18:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:24: #2 number of paired peaks: 1952 INFO @ Sun, 21 Jun 2020 18:03:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:24: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:03:24: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 18:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.20_model.r WARNING @ Sun, 21 Jun 2020 18:03:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:03:24: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 18:03:24: #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 18:03:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:03:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152100/SRX152100.20_summits.bed INFO @ Sun, 21 Jun 2020 18:03:46: Done! pass1 - making usageList (457 chroms): 1 millis pass2 - checking and writing primary data (1804 records, 4 fields): 14 millis CompletedMACS2peakCalling