Job ID = 6527782 SRX = SRX287583 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:59:06 prefetch.2.10.7: 1) Downloading 'SRR869726'... 2020-06-29T13:59:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:03:23 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:03:23 prefetch.2.10.7: 1) 'SRR869726' was downloaded successfully Read 22109731 spots for SRR869726/SRR869726.sra Written 22109731 spots for SRR869726/SRR869726.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: 00:07:55 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1293832 (5.85%) aligned 0 times 13813325 (62.48%) aligned exactly 1 time 7002574 (31.67%) aligned >1 times 94.15% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3521960 / 20815899 = 0.1692 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 @ Mon, 29 Jun 2020 23:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.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 @ Mon, 29 Jun 2020 23:22:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:22:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:22:42: 1000000 INFO @ Mon, 29 Jun 2020 23:22:48: 2000000 INFO @ Mon, 29 Jun 2020 23:22:54: 3000000 INFO @ Mon, 29 Jun 2020 23:22:59: 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 @ Mon, 29 Jun 2020 23:23:05: 5000000 INFO @ Mon, 29 Jun 2020 23:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.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 @ Mon, 29 Jun 2020 23:23:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:23:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:23:13: 6000000 INFO @ Mon, 29 Jun 2020 23:23:14: 1000000 INFO @ Mon, 29 Jun 2020 23:23:20: 7000000 INFO @ Mon, 29 Jun 2020 23:23:22: 2000000 INFO @ Mon, 29 Jun 2020 23:23:27: 8000000 INFO @ Mon, 29 Jun 2020 23:23:30: 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 @ Mon, 29 Jun 2020 23:23:35: 9000000 INFO @ Mon, 29 Jun 2020 23:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.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 @ Mon, 29 Jun 2020 23:23:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:23:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:23:38: 4000000 INFO @ Mon, 29 Jun 2020 23:23:42: 10000000 INFO @ Mon, 29 Jun 2020 23:23:43: 1000000 INFO @ Mon, 29 Jun 2020 23:23:46: 5000000 INFO @ Mon, 29 Jun 2020 23:23:49: 11000000 INFO @ Mon, 29 Jun 2020 23:23:51: 2000000 INFO @ Mon, 29 Jun 2020 23:23:54: 6000000 INFO @ Mon, 29 Jun 2020 23:23:57: 12000000 INFO @ Mon, 29 Jun 2020 23:23:58: 3000000 INFO @ Mon, 29 Jun 2020 23:24:02: 7000000 INFO @ Mon, 29 Jun 2020 23:24:04: 13000000 INFO @ Mon, 29 Jun 2020 23:24:05: 4000000 INFO @ Mon, 29 Jun 2020 23:24:09: 8000000 INFO @ Mon, 29 Jun 2020 23:24:12: 14000000 INFO @ Mon, 29 Jun 2020 23:24:13: 5000000 INFO @ Mon, 29 Jun 2020 23:24:17: 9000000 INFO @ Mon, 29 Jun 2020 23:24:20: 6000000 INFO @ Mon, 29 Jun 2020 23:24:20: 15000000 INFO @ Mon, 29 Jun 2020 23:24:25: 10000000 INFO @ Mon, 29 Jun 2020 23:24:27: 7000000 INFO @ Mon, 29 Jun 2020 23:24:28: 16000000 INFO @ Mon, 29 Jun 2020 23:24:33: 11000000 INFO @ Mon, 29 Jun 2020 23:24:35: 8000000 INFO @ Mon, 29 Jun 2020 23:24:35: 17000000 INFO @ Mon, 29 Jun 2020 23:24:37: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:24:37: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:24:37: #1 total tags in treatment: 17293939 INFO @ Mon, 29 Jun 2020 23:24:37: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:24:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:24:37: #1 tags after filtering in treatment: 17293939 INFO @ Mon, 29 Jun 2020 23:24:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:24:37: #1 finished! INFO @ Mon, 29 Jun 2020 23:24:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:24:38: #2 number of paired peaks: 195 WARNING @ Mon, 29 Jun 2020 23:24:38: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 29 Jun 2020 23:24:38: start model_add_line... INFO @ Mon, 29 Jun 2020 23:24:38: start X-correlation... INFO @ Mon, 29 Jun 2020 23:24:39: end of X-cor INFO @ Mon, 29 Jun 2020 23:24:39: #2 finished! INFO @ Mon, 29 Jun 2020 23:24:39: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:24:39: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 29 Jun 2020 23:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.05_model.r WARNING @ Mon, 29 Jun 2020 23:24:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:24:39: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 29 Jun 2020 23:24:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:24:39: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:24:40: 12000000 INFO @ Mon, 29 Jun 2020 23:24:42: 9000000 INFO @ Mon, 29 Jun 2020 23:24:48: 13000000 INFO @ Mon, 29 Jun 2020 23:24:49: 10000000 INFO @ Mon, 29 Jun 2020 23:24:56: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:24:57: 11000000 INFO @ Mon, 29 Jun 2020 23:25:03: 15000000 INFO @ Mon, 29 Jun 2020 23:25:04: 12000000 INFO @ Mon, 29 Jun 2020 23:25:11: 16000000 INFO @ Mon, 29 Jun 2020 23:25:11: 13000000 INFO @ Mon, 29 Jun 2020 23:25:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:25:18: 17000000 INFO @ Mon, 29 Jun 2020 23:25:19: 14000000 INFO @ Mon, 29 Jun 2020 23:25:20: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:25:20: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:25:20: #1 total tags in treatment: 17293939 INFO @ Mon, 29 Jun 2020 23:25:20: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:25:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:25:21: #1 tags after filtering in treatment: 17293939 INFO @ Mon, 29 Jun 2020 23:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:25:21: #1 finished! INFO @ Mon, 29 Jun 2020 23:25:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:25:22: #2 number of paired peaks: 195 WARNING @ Mon, 29 Jun 2020 23:25:22: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 29 Jun 2020 23:25:22: start model_add_line... INFO @ Mon, 29 Jun 2020 23:25:22: start X-correlation... INFO @ Mon, 29 Jun 2020 23:25:22: end of X-cor INFO @ Mon, 29 Jun 2020 23:25:22: #2 finished! INFO @ Mon, 29 Jun 2020 23:25:22: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:25:22: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 29 Jun 2020 23:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.10_model.r WARNING @ Mon, 29 Jun 2020 23:25:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:25:22: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 29 Jun 2020 23:25:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:25:22: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:25:27: 15000000 INFO @ Mon, 29 Jun 2020 23:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.05_summits.bed INFO @ Mon, 29 Jun 2020 23:25:29: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2173 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:25:33: 16000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:25:39: 17000000 INFO @ Mon, 29 Jun 2020 23:25:41: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:25:41: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:25:41: #1 total tags in treatment: 17293939 INFO @ Mon, 29 Jun 2020 23:25:41: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:25:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:25:42: #1 tags after filtering in treatment: 17293939 INFO @ Mon, 29 Jun 2020 23:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:25:42: #1 finished! INFO @ Mon, 29 Jun 2020 23:25:42: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:25:43: #2 number of paired peaks: 195 WARNING @ Mon, 29 Jun 2020 23:25:43: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 29 Jun 2020 23:25:43: start model_add_line... INFO @ Mon, 29 Jun 2020 23:25:43: start X-correlation... INFO @ Mon, 29 Jun 2020 23:25:43: end of X-cor INFO @ Mon, 29 Jun 2020 23:25:43: #2 finished! INFO @ Mon, 29 Jun 2020 23:25:43: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:25:43: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 29 Jun 2020 23:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.20_model.r WARNING @ Mon, 29 Jun 2020 23:25:43: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:25:43: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 29 Jun 2020 23:25:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:25:43: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:25:55: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:26:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:26:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.10_summits.bed INFO @ Mon, 29 Jun 2020 23:26:11: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1815 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:26:17: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287583/SRX287583.20_summits.bed INFO @ Mon, 29 Jun 2020 23:26:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1371 records, 4 fields): 3 millis CompletedMACS2peakCalling