Job ID = 14168125 SRX = ERX3978949 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18849051 spots for ERR3976019/ERR3976019.sra Written 18849051 spots for ERR3976019/ERR3976019.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169499 ("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: 02:26:25 18849051 reads; of these: 18849051 (100.00%) were paired; of these: 6813490 (36.15%) aligned concordantly 0 times 9121206 (48.39%) aligned concordantly exactly 1 time 2914355 (15.46%) aligned concordantly >1 times ---- 6813490 pairs aligned concordantly 0 times; of these: 474736 (6.97%) aligned discordantly 1 time ---- 6338754 pairs aligned 0 times concordantly or discordantly; of these: 12677508 mates make up the pairs; of these: 5834657 (46.02%) aligned 0 times 3803885 (30.00%) aligned exactly 1 time 3038966 (23.97%) aligned >1 times 84.52% overall alignment rate Time searching: 02:26:25 Overall time: 02:26:25 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 16 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] 9969903 / 12336183 = 0.8082 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 18:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.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 18:11:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:23: 1000000 INFO @ Fri, 10 Dec 2021 18:11:30: 2000000 INFO @ Fri, 10 Dec 2021 18:11:35: 3000000 INFO @ Fri, 10 Dec 2021 18:11:41: 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 18:11:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.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 18:11:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:47: 5000000 INFO @ Fri, 10 Dec 2021 18:11:53: 1000000 INFO @ Fri, 10 Dec 2021 18:11:53: 6000000 INFO @ Fri, 10 Dec 2021 18:12:00: 7000000 INFO @ Fri, 10 Dec 2021 18:12:00: 2000000 INFO @ Fri, 10 Dec 2021 18:12:06: 3000000 INFO @ Fri, 10 Dec 2021 18:12:06: 8000000 INFO @ Fri, 10 Dec 2021 18:12:13: 4000000 INFO @ Fri, 10 Dec 2021 18:12:13: 9000000 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 18:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.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 18:12:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:12:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:12:19: 5000000 INFO @ Fri, 10 Dec 2021 18:12:20: 10000000 INFO @ Fri, 10 Dec 2021 18:12:24: 1000000 INFO @ Fri, 10 Dec 2021 18:12:26: 6000000 INFO @ Fri, 10 Dec 2021 18:12:28: 11000000 INFO @ Fri, 10 Dec 2021 18:12:32: 2000000 INFO @ Fri, 10 Dec 2021 18:12:32: 7000000 INFO @ Fri, 10 Dec 2021 18:12:34: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:12:34: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:12:34: #1 total tags in treatment: 2359327 INFO @ Fri, 10 Dec 2021 18:12:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:12:34: #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 18:12:34: #1 tags after filtering in treatment: 2021388 INFO @ Fri, 10 Dec 2021 18:12:34: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 18:12:34: #1 finished! INFO @ Fri, 10 Dec 2021 18:12:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:12:35: #2 number of paired peaks: 3659 INFO @ Fri, 10 Dec 2021 18:12:35: start model_add_line... INFO @ Fri, 10 Dec 2021 18:12:35: start X-correlation... INFO @ Fri, 10 Dec 2021 18:12:35: end of X-cor INFO @ Fri, 10 Dec 2021 18:12:35: #2 finished! INFO @ Fri, 10 Dec 2021 18:12:35: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 18:12:35: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 18:12:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.05_model.r WARNING @ Fri, 10 Dec 2021 18:12:35: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:12:35: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Fri, 10 Dec 2021 18:12:35: #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 18:12:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:12:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:12:38: 3000000 INFO @ Fri, 10 Dec 2021 18:12:39: 8000000 INFO @ Fri, 10 Dec 2021 18:12:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.05_summits.bed INFO @ Fri, 10 Dec 2021 18:12:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6037 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:12:45: 4000000 INFO @ Fri, 10 Dec 2021 18:12:46: 9000000 INFO @ Fri, 10 Dec 2021 18:12:51: 5000000 INFO @ Fri, 10 Dec 2021 18:12:53: 10000000 INFO @ Fri, 10 Dec 2021 18:12:58: 6000000 INFO @ Fri, 10 Dec 2021 18:12:59: 11000000 INFO @ Fri, 10 Dec 2021 18:13:04: 7000000 INFO @ Fri, 10 Dec 2021 18:13:05: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:13:05: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:13:05: #1 total tags in treatment: 2359327 INFO @ Fri, 10 Dec 2021 18:13:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:05: #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 18:13:05: #1 tags after filtering in treatment: 2021388 INFO @ Fri, 10 Dec 2021 18:13:05: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 18:13:05: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:05: #2 number of paired peaks: 3659 INFO @ Fri, 10 Dec 2021 18:13:05: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:05: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:05: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:05: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:05: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 18:13:05: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 18:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.10_model.r WARNING @ Fri, 10 Dec 2021 18:13:05: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:13:05: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Fri, 10 Dec 2021 18:13:05: #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 18:13:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:13:11: 8000000 INFO @ Fri, 10 Dec 2021 18:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.10_summits.bed INFO @ Fri, 10 Dec 2021 18:13:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2197 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:13:18: 9000000 INFO @ Fri, 10 Dec 2021 18:13:24: 10000000 INFO @ Fri, 10 Dec 2021 18:13:30: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:13:36: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:13:36: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:13:36: #1 total tags in treatment: 2359327 INFO @ Fri, 10 Dec 2021 18:13:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:36: #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 18:13:36: #1 tags after filtering in treatment: 2021388 INFO @ Fri, 10 Dec 2021 18:13:36: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 18:13:36: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:36: #2 number of paired peaks: 3659 INFO @ Fri, 10 Dec 2021 18:13:36: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:36: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:36: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:36: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:36: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 18:13:36: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 18:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.20_model.r WARNING @ Fri, 10 Dec 2021 18:13:36: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:13:36: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Fri, 10 Dec 2021 18:13:36: #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 18:13:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978949/ERX3978949.20_summits.bed INFO @ Fri, 10 Dec 2021 18:13:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 3 millis CompletedMACS2peakCalling