Job ID = 6454299 SRX = SRX197571 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:14 prefetch.2.10.7: 1) Downloading 'SRR596999'... 2020-06-21T09:22:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:24:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:24:32 prefetch.2.10.7: 'SRR596999' is valid 2020-06-21T09:24:32 prefetch.2.10.7: 1) 'SRR596999' was downloaded successfully Read 20936152 spots for SRR596999/SRR596999.sra Written 20936152 spots for SRR596999/SRR596999.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: 00:04:45 20936152 reads; of these: 20936152 (100.00%) were unpaired; of these: 2593593 (12.39%) aligned 0 times 13282985 (63.45%) aligned exactly 1 time 5059574 (24.17%) aligned >1 times 87.61% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 8365380 / 18342559 = 0.4561 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 18:33:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.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 18:33:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:49: 1000000 INFO @ Sun, 21 Jun 2020 18:33:54: 2000000 INFO @ Sun, 21 Jun 2020 18:34:00: 3000000 INFO @ Sun, 21 Jun 2020 18:34:05: 4000000 INFO @ Sun, 21 Jun 2020 18:34:10: 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 18:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.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 18:34:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:15: 6000000 INFO @ Sun, 21 Jun 2020 18:34:20: 1000000 INFO @ Sun, 21 Jun 2020 18:34:21: 7000000 INFO @ Sun, 21 Jun 2020 18:34:26: 2000000 INFO @ Sun, 21 Jun 2020 18:34:27: 8000000 INFO @ Sun, 21 Jun 2020 18:34:31: 3000000 INFO @ Sun, 21 Jun 2020 18:34:32: 9000000 INFO @ Sun, 21 Jun 2020 18:34:37: 4000000 INFO @ Sun, 21 Jun 2020 18:34:38: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:34:38: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:34:38: #1 total tags in treatment: 9977179 INFO @ Sun, 21 Jun 2020 18:34:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:38: #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 18:34:38: #1 tags after filtering in treatment: 9977179 INFO @ Sun, 21 Jun 2020 18:34:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:39: #2 number of paired peaks: 1038 INFO @ Sun, 21 Jun 2020 18:34:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:39: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:34:39: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 18:34:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.05_model.r WARNING @ Sun, 21 Jun 2020 18:34:39: #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 18:34:39: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 18:34:39: #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 18:34:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:39: #3 Pre-compute pvalue-qvalue table... 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 18:34:42: 5000000 INFO @ Sun, 21 Jun 2020 18:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.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 18:34:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:48: 6000000 INFO @ Sun, 21 Jun 2020 18:34:50: 1000000 INFO @ Sun, 21 Jun 2020 18:34:53: 7000000 INFO @ Sun, 21 Jun 2020 18:34:55: 2000000 INFO @ Sun, 21 Jun 2020 18:34:59: 8000000 INFO @ Sun, 21 Jun 2020 18:34:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:01: 3000000 INFO @ Sun, 21 Jun 2020 18:35:05: 9000000 INFO @ Sun, 21 Jun 2020 18:35:07: 4000000 INFO @ Sun, 21 Jun 2020 18:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:09: Done! pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (4125 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:11: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:35:11: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:35:11: #1 total tags in treatment: 9977179 INFO @ Sun, 21 Jun 2020 18:35:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:11: #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 18:35:11: #1 tags after filtering in treatment: 9977179 INFO @ Sun, 21 Jun 2020 18:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:12: #2 number of paired peaks: 1038 INFO @ Sun, 21 Jun 2020 18:35:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:12: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:35:12: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 18:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.10_model.r WARNING @ Sun, 21 Jun 2020 18:35:12: #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 18:35:12: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 18:35:12: #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 18:35:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:12: 5000000 INFO @ Sun, 21 Jun 2020 18:35:17: 6000000 INFO @ Sun, 21 Jun 2020 18:35:23: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:35:28: 8000000 INFO @ Sun, 21 Jun 2020 18:35:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:34: 9000000 INFO @ Sun, 21 Jun 2020 18:35:39: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:35:39: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:35:39: #1 total tags in treatment: 9977179 INFO @ Sun, 21 Jun 2020 18:35:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:39: #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 18:35:39: #1 tags after filtering in treatment: 9977179 INFO @ Sun, 21 Jun 2020 18:35:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:40: #2 number of paired peaks: 1038 INFO @ Sun, 21 Jun 2020 18:35:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:40: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:35:40: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 18:35:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.20_model.r WARNING @ Sun, 21 Jun 2020 18:35:40: #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 18:35:40: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 18:35:40: #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 18:35:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:42: Done! pass1 - making usageList (554 chroms): 2 millis pass2 - checking and writing primary data (2662 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:36:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197571/SRX197571.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:11: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 10 millis CompletedMACS2peakCalling