Job ID = 14168342 SRX = ERX3978856 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34244933 spots for ERR3975925/ERR3975925.sra Written 34244933 spots for ERR3975925/ERR3975925.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169687 ("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: 01:30:06 34244933 reads; of these: 34244933 (100.00%) were paired; of these: 4293476 (12.54%) aligned concordantly 0 times 24145725 (70.51%) aligned concordantly exactly 1 time 5805732 (16.95%) aligned concordantly >1 times ---- 4293476 pairs aligned concordantly 0 times; of these: 943263 (21.97%) aligned discordantly 1 time ---- 3350213 pairs aligned 0 times concordantly or discordantly; of these: 6700426 mates make up the pairs; of these: 3196120 (47.70%) aligned 0 times 1700631 (25.38%) aligned exactly 1 time 1803675 (26.92%) aligned >1 times 95.33% overall alignment rate Time searching: 01:30:06 Overall time: 01:30:06 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] 24619937 / 30782509 = 0.7998 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 19:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.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 19:32:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:32:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:32:13: 1000000 INFO @ Fri, 10 Dec 2021 19:32:21: 2000000 INFO @ Fri, 10 Dec 2021 19:32:29: 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 19:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.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 19:32:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:32:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:32:37: 4000000 INFO @ Fri, 10 Dec 2021 19:32:44: 1000000 INFO @ Fri, 10 Dec 2021 19:32:45: 5000000 INFO @ Fri, 10 Dec 2021 19:32:53: 2000000 INFO @ Fri, 10 Dec 2021 19:32:54: 6000000 INFO @ Fri, 10 Dec 2021 19:33:01: 3000000 INFO @ Fri, 10 Dec 2021 19:33:03: 7000000 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 19:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.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 19:33:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:33:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:33:10: 4000000 INFO @ Fri, 10 Dec 2021 19:33:11: 8000000 INFO @ Fri, 10 Dec 2021 19:33:14: 1000000 INFO @ Fri, 10 Dec 2021 19:33:18: 5000000 INFO @ Fri, 10 Dec 2021 19:33:20: 9000000 INFO @ Fri, 10 Dec 2021 19:33:23: 2000000 INFO @ Fri, 10 Dec 2021 19:33:27: 6000000 INFO @ Fri, 10 Dec 2021 19:33:29: 10000000 INFO @ Fri, 10 Dec 2021 19:33:32: 3000000 INFO @ Fri, 10 Dec 2021 19:33:36: 7000000 INFO @ Fri, 10 Dec 2021 19:33:39: 11000000 INFO @ Fri, 10 Dec 2021 19:33:41: 4000000 INFO @ Fri, 10 Dec 2021 19:33:45: 8000000 INFO @ Fri, 10 Dec 2021 19:33:48: 12000000 INFO @ Fri, 10 Dec 2021 19:33:50: 5000000 INFO @ Fri, 10 Dec 2021 19:33:54: 9000000 INFO @ Fri, 10 Dec 2021 19:33:57: 13000000 INFO @ Fri, 10 Dec 2021 19:33:59: 6000000 INFO @ Fri, 10 Dec 2021 19:34:03: 10000000 INFO @ Fri, 10 Dec 2021 19:34:06: 14000000 INFO @ Fri, 10 Dec 2021 19:34:08: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:34:12: 11000000 INFO @ Fri, 10 Dec 2021 19:34:15: 15000000 INFO @ Fri, 10 Dec 2021 19:34:17: 8000000 INFO @ Fri, 10 Dec 2021 19:34:21: 12000000 INFO @ Fri, 10 Dec 2021 19:34:24: 16000000 INFO @ Fri, 10 Dec 2021 19:34:25: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:34:25: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:34:25: #1 total tags in treatment: 5961543 INFO @ Fri, 10 Dec 2021 19:34:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:34:25: #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 19:34:25: #1 tags after filtering in treatment: 5181935 INFO @ Fri, 10 Dec 2021 19:34:25: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 19:34:25: #1 finished! INFO @ Fri, 10 Dec 2021 19:34:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:34:25: #2 number of paired peaks: 6173 INFO @ Fri, 10 Dec 2021 19:34:25: start model_add_line... INFO @ Fri, 10 Dec 2021 19:34:25: start X-correlation... INFO @ Fri, 10 Dec 2021 19:34:25: end of X-cor INFO @ Fri, 10 Dec 2021 19:34:25: #2 finished! INFO @ Fri, 10 Dec 2021 19:34:25: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 19:34:25: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 19:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.05_model.r INFO @ Fri, 10 Dec 2021 19:34:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:34:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:34:26: 9000000 INFO @ Fri, 10 Dec 2021 19:34:30: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:34:35: 10000000 INFO @ Fri, 10 Dec 2021 19:34:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:34:39: 14000000 INFO @ Fri, 10 Dec 2021 19:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.05_summits.bed INFO @ Fri, 10 Dec 2021 19:34:44: Done! INFO @ Fri, 10 Dec 2021 19:34:44: 11000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10589 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:34:48: 15000000 INFO @ Fri, 10 Dec 2021 19:34:53: 12000000 INFO @ Fri, 10 Dec 2021 19:34:56: 16000000 INFO @ Fri, 10 Dec 2021 19:34:57: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:34:57: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:34:57: #1 total tags in treatment: 5961543 INFO @ Fri, 10 Dec 2021 19:34:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:34:57: #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 19:34:57: #1 tags after filtering in treatment: 5181935 INFO @ Fri, 10 Dec 2021 19:34:57: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 19:34:57: #1 finished! INFO @ Fri, 10 Dec 2021 19:34:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:34:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:34:57: #2 number of paired peaks: 6173 INFO @ Fri, 10 Dec 2021 19:34:57: start model_add_line... INFO @ Fri, 10 Dec 2021 19:34:58: start X-correlation... INFO @ Fri, 10 Dec 2021 19:34:58: end of X-cor INFO @ Fri, 10 Dec 2021 19:34:58: #2 finished! INFO @ Fri, 10 Dec 2021 19:34:58: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 19:34:58: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 19:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.10_model.r INFO @ Fri, 10 Dec 2021 19:34:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:35:02: 13000000 INFO @ Fri, 10 Dec 2021 19:35:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:35:10: 14000000 INFO @ Fri, 10 Dec 2021 19:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:35:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:35:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.10_summits.bed INFO @ Fri, 10 Dec 2021 19:35:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7758 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:35:19: 15000000 INFO @ Fri, 10 Dec 2021 19:35:26: 16000000 INFO @ Fri, 10 Dec 2021 19:35:27: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:35:27: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:35:27: #1 total tags in treatment: 5961543 INFO @ Fri, 10 Dec 2021 19:35:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:35:27: #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 19:35:27: #1 tags after filtering in treatment: 5181935 INFO @ Fri, 10 Dec 2021 19:35:27: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 10 Dec 2021 19:35:27: #1 finished! INFO @ Fri, 10 Dec 2021 19:35:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:35:28: #2 number of paired peaks: 6173 INFO @ Fri, 10 Dec 2021 19:35:28: start model_add_line... INFO @ Fri, 10 Dec 2021 19:35:28: start X-correlation... INFO @ Fri, 10 Dec 2021 19:35:28: end of X-cor INFO @ Fri, 10 Dec 2021 19:35:28: #2 finished! INFO @ Fri, 10 Dec 2021 19:35:28: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 19:35:28: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 19:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.20_model.r INFO @ Fri, 10 Dec 2021 19:35:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:35:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978856/ERX3978856.20_summits.bed INFO @ Fri, 10 Dec 2021 19:35:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5020 records, 4 fields): 9 millis CompletedMACS2peakCalling