Job ID = 14168124 SRX = ERX3978948 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29625029 spots for ERR3976018/ERR3976018.sra Written 29625029 spots for ERR3976018/ERR3976018.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169280 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:34:30 29625029 reads; of these: 29625029 (100.00%) were paired; of these: 3926255 (13.25%) aligned concordantly 0 times 20502640 (69.21%) aligned concordantly exactly 1 time 5196134 (17.54%) aligned concordantly >1 times ---- 3926255 pairs aligned concordantly 0 times; of these: 1102629 (28.08%) aligned discordantly 1 time ---- 2823626 pairs aligned 0 times concordantly or discordantly; of these: 5647252 mates make up the pairs; of these: 2568932 (45.49%) aligned 0 times 1469516 (26.02%) aligned exactly 1 time 1608804 (28.49%) aligned >1 times 95.66% overall alignment rate Time searching: 01:34:30 Overall time: 01:34:30 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 24 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 19550915 / 26722075 = 0.7316 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 17:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.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 @ Fri, 10 Dec 2021 17:20:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:20:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:21:03: 1000000 INFO @ Fri, 10 Dec 2021 17:21:09: 2000000 INFO @ Fri, 10 Dec 2021 17:21:15: 3000000 INFO @ Fri, 10 Dec 2021 17:21:21: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 17:21:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.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 @ Fri, 10 Dec 2021 17:21:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:21:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:21:27: 5000000 INFO @ Fri, 10 Dec 2021 17:21:32: 1000000 INFO @ Fri, 10 Dec 2021 17:21:33: 6000000 INFO @ Fri, 10 Dec 2021 17:21:38: 2000000 INFO @ Fri, 10 Dec 2021 17:21:39: 7000000 INFO @ Fri, 10 Dec 2021 17:21:43: 3000000 INFO @ Fri, 10 Dec 2021 17:21:45: 8000000 INFO @ Fri, 10 Dec 2021 17:21:48: 4000000 INFO @ Fri, 10 Dec 2021 17:21:51: 9000000 INFO @ Fri, 10 Dec 2021 17:21:54: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 17:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.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 @ Fri, 10 Dec 2021 17:21:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:21:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:21:58: 10000000 INFO @ Fri, 10 Dec 2021 17:21:59: 6000000 INFO @ Fri, 10 Dec 2021 17:22:02: 1000000 INFO @ Fri, 10 Dec 2021 17:22:04: 11000000 INFO @ Fri, 10 Dec 2021 17:22:04: 7000000 INFO @ Fri, 10 Dec 2021 17:22:08: 2000000 INFO @ Fri, 10 Dec 2021 17:22:10: 8000000 INFO @ Fri, 10 Dec 2021 17:22:10: 12000000 INFO @ Fri, 10 Dec 2021 17:22:13: 3000000 INFO @ Fri, 10 Dec 2021 17:22:15: 9000000 INFO @ Fri, 10 Dec 2021 17:22:16: 13000000 INFO @ Fri, 10 Dec 2021 17:22:18: 4000000 INFO @ Fri, 10 Dec 2021 17:22:21: 10000000 INFO @ Fri, 10 Dec 2021 17:22:23: 14000000 INFO @ Fri, 10 Dec 2021 17:22:24: 5000000 INFO @ Fri, 10 Dec 2021 17:22:27: 11000000 INFO @ Fri, 10 Dec 2021 17:22:29: 15000000 INFO @ Fri, 10 Dec 2021 17:22:30: 6000000 INFO @ Fri, 10 Dec 2021 17:22:33: 12000000 INFO @ Fri, 10 Dec 2021 17:22:35: 16000000 INFO @ Fri, 10 Dec 2021 17:22:35: 7000000 INFO @ Fri, 10 Dec 2021 17:22:39: 13000000 INFO @ Fri, 10 Dec 2021 17:22:40: 8000000 INFO @ Fri, 10 Dec 2021 17:22:41: 17000000 INFO @ Fri, 10 Dec 2021 17:22:45: 14000000 INFO @ Fri, 10 Dec 2021 17:22:45: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:22:45: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:22:45: #1 total tags in treatment: 6755774 INFO @ Fri, 10 Dec 2021 17:22:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:22:45: #1 tags after filtering in treatment: 6137755 INFO @ Fri, 10 Dec 2021 17:22:45: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 17:22:45: #1 finished! INFO @ Fri, 10 Dec 2021 17:22:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:22:45: #2 number of paired peaks: 1142 INFO @ Fri, 10 Dec 2021 17:22:45: start model_add_line... INFO @ Fri, 10 Dec 2021 17:22:45: start X-correlation... INFO @ Fri, 10 Dec 2021 17:22:45: end of X-cor INFO @ Fri, 10 Dec 2021 17:22:45: #2 finished! INFO @ Fri, 10 Dec 2021 17:22:45: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Dec 2021 17:22:45: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Dec 2021 17:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.05_model.r WARNING @ Fri, 10 Dec 2021 17:22:45: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:22:45: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Fri, 10 Dec 2021 17:22:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:22:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:22:46: 9000000 INFO @ Fri, 10 Dec 2021 17:22:51: 15000000 INFO @ Fri, 10 Dec 2021 17:22:51: 10000000 INFO @ Fri, 10 Dec 2021 17:22:57: 16000000 INFO @ Fri, 10 Dec 2021 17:22:57: 11000000 INFO @ Fri, 10 Dec 2021 17:22:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:23:02: 17000000 INFO @ Fri, 10 Dec 2021 17:23:02: 12000000 INFO @ Fri, 10 Dec 2021 17:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:23:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:23:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.05_summits.bed INFO @ Fri, 10 Dec 2021 17:23:06: Done! INFO @ Fri, 10 Dec 2021 17:23:06: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:23:06: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:23:06: #1 total tags in treatment: 6755774 INFO @ Fri, 10 Dec 2021 17:23:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:23:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:23:06: #1 tags after filtering in treatment: 6137755 INFO @ Fri, 10 Dec 2021 17:23:06: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 17:23:06: #1 finished! INFO @ Fri, 10 Dec 2021 17:23:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:23:06: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6197 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:23:06: #2 number of paired peaks: 1142 INFO @ Fri, 10 Dec 2021 17:23:06: start model_add_line... INFO @ Fri, 10 Dec 2021 17:23:06: start X-correlation... INFO @ Fri, 10 Dec 2021 17:23:06: end of X-cor INFO @ Fri, 10 Dec 2021 17:23:06: #2 finished! INFO @ Fri, 10 Dec 2021 17:23:06: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Dec 2021 17:23:06: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Dec 2021 17:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.10_model.r WARNING @ Fri, 10 Dec 2021 17:23:07: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:23:07: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Fri, 10 Dec 2021 17:23:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:23:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:23:08: 13000000 INFO @ Fri, 10 Dec 2021 17:23:13: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:23:19: 15000000 INFO @ Fri, 10 Dec 2021 17:23:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:23:24: 16000000 INFO @ Fri, 10 Dec 2021 17:23:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:23:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.10_summits.bed INFO @ Fri, 10 Dec 2021 17:23:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2830 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:23:29: 17000000 INFO @ Fri, 10 Dec 2021 17:23:32: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:23:32: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:23:32: #1 total tags in treatment: 6755774 INFO @ Fri, 10 Dec 2021 17:23:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:23:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:23:32: #1 tags after filtering in treatment: 6137755 INFO @ Fri, 10 Dec 2021 17:23:32: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 17:23:32: #1 finished! INFO @ Fri, 10 Dec 2021 17:23:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:23:32: #2 number of paired peaks: 1142 INFO @ Fri, 10 Dec 2021 17:23:32: start model_add_line... INFO @ Fri, 10 Dec 2021 17:23:33: start X-correlation... INFO @ Fri, 10 Dec 2021 17:23:33: end of X-cor INFO @ Fri, 10 Dec 2021 17:23:33: #2 finished! INFO @ Fri, 10 Dec 2021 17:23:33: #2 predicted fragment length is 160 bps INFO @ Fri, 10 Dec 2021 17:23:33: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 10 Dec 2021 17:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.20_model.r WARNING @ Fri, 10 Dec 2021 17:23:33: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:23:33: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Fri, 10 Dec 2021 17:23:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:23:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:23:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:23:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978948/ERX3978948.20_summits.bed INFO @ Fri, 10 Dec 2021 17:23:52: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1133 records, 4 fields): 4 millis CompletedMACS2peakCalling