Job ID = 14168699 SRX = ERX3978762 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11828272 spots for ERR3975777/ERR3975777.sra Written 11828272 spots for ERR3975777/ERR3975777.sra Read 12953332 spots for ERR3975804/ERR3975804.sra Written 12953332 spots for ERR3975804/ERR3975804.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169836 ("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: 00:40:27 24781604 reads; of these: 24781604 (100.00%) were paired; of these: 10884981 (43.92%) aligned concordantly 0 times 5779001 (23.32%) aligned concordantly exactly 1 time 8117622 (32.76%) aligned concordantly >1 times ---- 10884981 pairs aligned concordantly 0 times; of these: 1440270 (13.23%) aligned discordantly 1 time ---- 9444711 pairs aligned 0 times concordantly or discordantly; of these: 18889422 mates make up the pairs; of these: 11444427 (60.59%) aligned 0 times 413803 (2.19%) aligned exactly 1 time 7031192 (37.22%) aligned >1 times 76.91% overall alignment rate Time searching: 00:40:27 Overall time: 00:40:27 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 28 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] 6868287 / 15172679 = 0.4527 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 20:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.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 20:17:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:17:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:18:02: 1000000 INFO @ Fri, 10 Dec 2021 20:18:11: 2000000 INFO @ Fri, 10 Dec 2021 20:18:20: 3000000 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 20:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.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 20:18:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:18:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:18:31: 4000000 INFO @ Fri, 10 Dec 2021 20:18:31: 1000000 INFO @ Fri, 10 Dec 2021 20:18:40: 2000000 INFO @ Fri, 10 Dec 2021 20:18:41: 5000000 INFO @ Fri, 10 Dec 2021 20:18:49: 3000000 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 20:18:52: 6000000 INFO @ Fri, 10 Dec 2021 20:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.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 20:18:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:18:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:18:58: 4000000 INFO @ Fri, 10 Dec 2021 20:19:03: 1000000 INFO @ Fri, 10 Dec 2021 20:19:03: 7000000 INFO @ Fri, 10 Dec 2021 20:19:07: 5000000 INFO @ Fri, 10 Dec 2021 20:19:14: 2000000 INFO @ Fri, 10 Dec 2021 20:19:14: 8000000 INFO @ Fri, 10 Dec 2021 20:19:17: 6000000 INFO @ Fri, 10 Dec 2021 20:19:24: 3000000 INFO @ Fri, 10 Dec 2021 20:19:24: 9000000 INFO @ Fri, 10 Dec 2021 20:19:26: 7000000 INFO @ Fri, 10 Dec 2021 20:19:35: 4000000 INFO @ Fri, 10 Dec 2021 20:19:35: 8000000 INFO @ Fri, 10 Dec 2021 20:19:35: 10000000 INFO @ Fri, 10 Dec 2021 20:19:44: 9000000 INFO @ Fri, 10 Dec 2021 20:19:45: 5000000 INFO @ Fri, 10 Dec 2021 20:19:46: 11000000 INFO @ Fri, 10 Dec 2021 20:19:53: 10000000 INFO @ Fri, 10 Dec 2021 20:19:56: 6000000 INFO @ Fri, 10 Dec 2021 20:19:57: 12000000 INFO @ Fri, 10 Dec 2021 20:20:02: 11000000 INFO @ Fri, 10 Dec 2021 20:20:07: 7000000 INFO @ Fri, 10 Dec 2021 20:20:07: 13000000 INFO @ Fri, 10 Dec 2021 20:20:11: 12000000 INFO @ Fri, 10 Dec 2021 20:20:17: 8000000 INFO @ Fri, 10 Dec 2021 20:20:18: 14000000 INFO @ Fri, 10 Dec 2021 20:20:20: 13000000 INFO @ Fri, 10 Dec 2021 20:20:28: 9000000 INFO @ Fri, 10 Dec 2021 20:20:28: 15000000 INFO @ Fri, 10 Dec 2021 20:20:29: 14000000 INFO @ Fri, 10 Dec 2021 20:20:37: 15000000 INFO @ Fri, 10 Dec 2021 20:20:38: 10000000 INFO @ Fri, 10 Dec 2021 20:20:38: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:20:46: 16000000 INFO @ Fri, 10 Dec 2021 20:20:49: 17000000 INFO @ Fri, 10 Dec 2021 20:20:49: 11000000 INFO @ Fri, 10 Dec 2021 20:20:55: 17000000 INFO @ Fri, 10 Dec 2021 20:20:59: 18000000 INFO @ Fri, 10 Dec 2021 20:21:00: 12000000 INFO @ Fri, 10 Dec 2021 20:21:04: 18000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:21:10: 19000000 INFO @ Fri, 10 Dec 2021 20:21:10: 13000000 INFO @ Fri, 10 Dec 2021 20:21:13: 19000000 INFO @ Fri, 10 Dec 2021 20:21:20: 20000000 INFO @ Fri, 10 Dec 2021 20:21:20: 14000000 INFO @ Fri, 10 Dec 2021 20:21:22: 20000000 INFO @ Fri, 10 Dec 2021 20:21:30: 21000000 INFO @ Fri, 10 Dec 2021 20:21:30: 15000000 INFO @ Fri, 10 Dec 2021 20:21:31: 21000000 INFO @ Fri, 10 Dec 2021 20:21:41: 16000000 INFO @ Fri, 10 Dec 2021 20:21:41: 22000000 INFO @ Fri, 10 Dec 2021 20:21:42: 22000000 INFO @ Fri, 10 Dec 2021 20:21:51: 17000000 INFO @ Fri, 10 Dec 2021 20:21:52: 23000000 INFO @ Fri, 10 Dec 2021 20:21:53: 23000000 INFO @ Fri, 10 Dec 2021 20:22:01: 18000000 INFO @ Fri, 10 Dec 2021 20:22:02: 24000000 INFO @ Fri, 10 Dec 2021 20:22:03: 24000000 INFO @ Fri, 10 Dec 2021 20:22:06: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:22:06: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:22:06: #1 total tags in treatment: 7225959 INFO @ Fri, 10 Dec 2021 20:22:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:22:06: #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 20:22:07: #1 tags after filtering in treatment: 5401958 INFO @ Fri, 10 Dec 2021 20:22:07: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 20:22:07: #1 finished! INFO @ Fri, 10 Dec 2021 20:22:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:22:07: #2 number of paired peaks: 2809 INFO @ Fri, 10 Dec 2021 20:22:07: start model_add_line... INFO @ Fri, 10 Dec 2021 20:22:07: start X-correlation... INFO @ Fri, 10 Dec 2021 20:22:07: end of X-cor INFO @ Fri, 10 Dec 2021 20:22:07: #2 finished! INFO @ Fri, 10 Dec 2021 20:22:07: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Dec 2021 20:22:07: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Dec 2021 20:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.05_model.r WARNING @ Fri, 10 Dec 2021 20:22:07: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:22:07: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Fri, 10 Dec 2021 20:22:07: #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 20:22:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:22:07: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:22:07: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:22:07: #1 total tags in treatment: 7225959 INFO @ Fri, 10 Dec 2021 20:22:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:22:07: #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 20:22:07: #1 tags after filtering in treatment: 5401958 INFO @ Fri, 10 Dec 2021 20:22:07: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 20:22:07: #1 finished! INFO @ Fri, 10 Dec 2021 20:22:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:22:08: #2 number of paired peaks: 2809 INFO @ Fri, 10 Dec 2021 20:22:08: start model_add_line... INFO @ Fri, 10 Dec 2021 20:22:08: start X-correlation... INFO @ Fri, 10 Dec 2021 20:22:08: end of X-cor INFO @ Fri, 10 Dec 2021 20:22:08: #2 finished! INFO @ Fri, 10 Dec 2021 20:22:08: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Dec 2021 20:22:08: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Dec 2021 20:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.10_model.r WARNING @ Fri, 10 Dec 2021 20:22:08: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:22:08: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Fri, 10 Dec 2021 20:22:08: #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 20:22:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:22:11: 19000000 INFO @ Fri, 10 Dec 2021 20:22:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:22:20: 20000000 INFO @ Fri, 10 Dec 2021 20:22:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:22:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:22:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:22:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.05_summits.bed INFO @ Fri, 10 Dec 2021 20:22:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8542 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.10_summits.bed INFO @ Fri, 10 Dec 2021 20:22:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4429 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:22:29: 21000000 INFO @ Fri, 10 Dec 2021 20:22:39: 22000000 INFO @ Fri, 10 Dec 2021 20:22:48: 23000000 INFO @ Fri, 10 Dec 2021 20:22:57: 24000000 INFO @ Fri, 10 Dec 2021 20:23:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:23:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:23:01: #1 total tags in treatment: 7225959 INFO @ Fri, 10 Dec 2021 20:23:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:23:01: #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 20:23:01: #1 tags after filtering in treatment: 5401958 INFO @ Fri, 10 Dec 2021 20:23:01: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 20:23:01: #1 finished! INFO @ Fri, 10 Dec 2021 20:23:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:23:01: #2 number of paired peaks: 2809 INFO @ Fri, 10 Dec 2021 20:23:01: start model_add_line... INFO @ Fri, 10 Dec 2021 20:23:01: start X-correlation... INFO @ Fri, 10 Dec 2021 20:23:02: end of X-cor INFO @ Fri, 10 Dec 2021 20:23:02: #2 finished! INFO @ Fri, 10 Dec 2021 20:23:02: #2 predicted fragment length is 183 bps INFO @ Fri, 10 Dec 2021 20:23:02: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 10 Dec 2021 20:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.20_model.r WARNING @ Fri, 10 Dec 2021 20:23:02: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:23:02: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Fri, 10 Dec 2021 20:23:02: #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 20:23:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:23:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:23:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:23:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:23:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978762/ERX3978762.20_summits.bed INFO @ Fri, 10 Dec 2021 20:23:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1546 records, 4 fields): 3 millis CompletedMACS2peakCalling