Job ID = 14168034 SRX = ERX3978931 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 39209564 spots for ERR3976001/ERR3976001.sra Written 39209564 spots for ERR3976001/ERR3976001.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169062 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:46:40 39209564 reads; of these: 39209564 (100.00%) were paired; of these: 5566225 (14.20%) aligned concordantly 0 times 24927987 (63.58%) aligned concordantly exactly 1 time 8715352 (22.23%) aligned concordantly >1 times ---- 5566225 pairs aligned concordantly 0 times; of these: 642141 (11.54%) aligned discordantly 1 time ---- 4924084 pairs aligned 0 times concordantly or discordantly; of these: 9848168 mates make up the pairs; of these: 6072921 (61.67%) aligned 0 times 1784833 (18.12%) aligned exactly 1 time 1990414 (20.21%) aligned >1 times 92.26% overall alignment rate Time searching: 01:46:41 Overall time: 01:46:41 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 32 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] 20960375 / 34124532 = 0.6142 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 16:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.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 16:42:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:42:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:42:58: 1000000 INFO @ Fri, 10 Dec 2021 16:43:04: 2000000 INFO @ Fri, 10 Dec 2021 16:43:11: 3000000 INFO @ Fri, 10 Dec 2021 16:43:17: 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 16:43:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.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 16:43:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:43:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:43:23: 5000000 INFO @ Fri, 10 Dec 2021 16:43:31: 1000000 INFO @ Fri, 10 Dec 2021 16:43:31: 6000000 INFO @ Fri, 10 Dec 2021 16:43:39: 7000000 INFO @ Fri, 10 Dec 2021 16:43:40: 2000000 INFO @ Fri, 10 Dec 2021 16:43:47: 8000000 INFO @ Fri, 10 Dec 2021 16:43:49: 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 16:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.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 16:43:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:43:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:43:55: 9000000 INFO @ Fri, 10 Dec 2021 16:43:58: 4000000 INFO @ Fri, 10 Dec 2021 16:44:00: 1000000 INFO @ Fri, 10 Dec 2021 16:44:03: 10000000 INFO @ Fri, 10 Dec 2021 16:44:07: 5000000 INFO @ Fri, 10 Dec 2021 16:44:08: 2000000 INFO @ Fri, 10 Dec 2021 16:44:11: 11000000 INFO @ Fri, 10 Dec 2021 16:44:16: 6000000 INFO @ Fri, 10 Dec 2021 16:44:17: 3000000 INFO @ Fri, 10 Dec 2021 16:44:20: 12000000 INFO @ Fri, 10 Dec 2021 16:44:25: 7000000 INFO @ Fri, 10 Dec 2021 16:44:25: 4000000 INFO @ Fri, 10 Dec 2021 16:44:28: 13000000 INFO @ Fri, 10 Dec 2021 16:44:34: 5000000 INFO @ Fri, 10 Dec 2021 16:44:34: 8000000 INFO @ Fri, 10 Dec 2021 16:44:36: 14000000 INFO @ Fri, 10 Dec 2021 16:44:42: 6000000 INFO @ Fri, 10 Dec 2021 16:44:42: 9000000 INFO @ Fri, 10 Dec 2021 16:44:45: 15000000 INFO @ Fri, 10 Dec 2021 16:44:50: 7000000 INFO @ Fri, 10 Dec 2021 16:44:51: 10000000 INFO @ Fri, 10 Dec 2021 16:44:53: 16000000 INFO @ Fri, 10 Dec 2021 16:44:59: 8000000 INFO @ Fri, 10 Dec 2021 16:45:00: 11000000 INFO @ Fri, 10 Dec 2021 16:45:01: 17000000 INFO @ Fri, 10 Dec 2021 16:45:07: 9000000 INFO @ Fri, 10 Dec 2021 16:45:09: 12000000 INFO @ Fri, 10 Dec 2021 16:45:10: 18000000 INFO @ Fri, 10 Dec 2021 16:45:15: 10000000 INFO @ Fri, 10 Dec 2021 16:45:18: 13000000 INFO @ Fri, 10 Dec 2021 16:45:19: 19000000 INFO @ Fri, 10 Dec 2021 16:45:23: 11000000 INFO @ Fri, 10 Dec 2021 16:45:27: 14000000 INFO @ Fri, 10 Dec 2021 16:45:28: 20000000 INFO @ Fri, 10 Dec 2021 16:45:31: 12000000 INFO @ Fri, 10 Dec 2021 16:45:36: 15000000 INFO @ Fri, 10 Dec 2021 16:45:37: 21000000 INFO @ Fri, 10 Dec 2021 16:45:39: 13000000 INFO @ Fri, 10 Dec 2021 16:45:45: 16000000 INFO @ Fri, 10 Dec 2021 16:45:45: 22000000 INFO @ Fri, 10 Dec 2021 16:45:47: 14000000 INFO @ Fri, 10 Dec 2021 16:45:53: 17000000 INFO @ Fri, 10 Dec 2021 16:45:54: 23000000 INFO @ Fri, 10 Dec 2021 16:45:55: 15000000 INFO @ Fri, 10 Dec 2021 16:46:02: 18000000 INFO @ Fri, 10 Dec 2021 16:46:03: 16000000 INFO @ Fri, 10 Dec 2021 16:46:03: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:46:11: 19000000 INFO @ Fri, 10 Dec 2021 16:46:11: 17000000 INFO @ Fri, 10 Dec 2021 16:46:12: 25000000 INFO @ Fri, 10 Dec 2021 16:46:19: 18000000 INFO @ Fri, 10 Dec 2021 16:46:20: 20000000 INFO @ Fri, 10 Dec 2021 16:46:21: 26000000 INFO @ Fri, 10 Dec 2021 16:46:27: 19000000 INFO @ Fri, 10 Dec 2021 16:46:28: 21000000 INFO @ Fri, 10 Dec 2021 16:46:30: 27000000 INFO @ Fri, 10 Dec 2021 16:46:35: 20000000 INFO @ Fri, 10 Dec 2021 16:46:37: 22000000 INFO @ Fri, 10 Dec 2021 16:46:39: 28000000 INFO @ Fri, 10 Dec 2021 16:46:43: 21000000 INFO @ Fri, 10 Dec 2021 16:46:46: 23000000 INFO @ Fri, 10 Dec 2021 16:46:47: 29000000 INFO @ Fri, 10 Dec 2021 16:46:51: 22000000 INFO @ Fri, 10 Dec 2021 16:46:55: 24000000 INFO @ Fri, 10 Dec 2021 16:46:56: 30000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:46:59: 23000000 INFO @ Fri, 10 Dec 2021 16:47:00: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:47:00: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:47:00: #1 total tags in treatment: 13080355 INFO @ Fri, 10 Dec 2021 16:47:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:47:00: #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 16:47:00: #1 tags after filtering in treatment: 11673899 INFO @ Fri, 10 Dec 2021 16:47:00: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 16:47:00: #1 finished! INFO @ Fri, 10 Dec 2021 16:47:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:47:01: #2 number of paired peaks: 1010 INFO @ Fri, 10 Dec 2021 16:47:01: start model_add_line... INFO @ Fri, 10 Dec 2021 16:47:01: start X-correlation... INFO @ Fri, 10 Dec 2021 16:47:01: end of X-cor INFO @ Fri, 10 Dec 2021 16:47:01: #2 finished! INFO @ Fri, 10 Dec 2021 16:47:01: #2 predicted fragment length is 165 bps INFO @ Fri, 10 Dec 2021 16:47:01: #2 alternative fragment length(s) may be 165 bps INFO @ Fri, 10 Dec 2021 16:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.05_model.r INFO @ Fri, 10 Dec 2021 16:47:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:47:03: 25000000 INFO @ Fri, 10 Dec 2021 16:47:07: 24000000 INFO @ Fri, 10 Dec 2021 16:47:12: 26000000 INFO @ Fri, 10 Dec 2021 16:47:14: 25000000 INFO @ Fri, 10 Dec 2021 16:47:21: 27000000 INFO @ Fri, 10 Dec 2021 16:47:22: 26000000 INFO @ Fri, 10 Dec 2021 16:47:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:47:29: 28000000 INFO @ Fri, 10 Dec 2021 16:47:30: 27000000 INFO @ Fri, 10 Dec 2021 16:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:47:38: 29000000 INFO @ Fri, 10 Dec 2021 16:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.05_summits.bed INFO @ Fri, 10 Dec 2021 16:47:38: Done! INFO @ Fri, 10 Dec 2021 16:47:38: 28000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10082 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:47:46: 29000000 INFO @ Fri, 10 Dec 2021 16:47:46: 30000000 INFO @ Fri, 10 Dec 2021 16:47:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:47:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:47:50: #1 total tags in treatment: 13080355 INFO @ Fri, 10 Dec 2021 16:47:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:47:50: #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 16:47:50: #1 tags after filtering in treatment: 11673899 INFO @ Fri, 10 Dec 2021 16:47:50: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 16:47:50: #1 finished! INFO @ Fri, 10 Dec 2021 16:47:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:47:51: #2 number of paired peaks: 1010 INFO @ Fri, 10 Dec 2021 16:47:51: start model_add_line... INFO @ Fri, 10 Dec 2021 16:47:51: start X-correlation... INFO @ Fri, 10 Dec 2021 16:47:51: end of X-cor INFO @ Fri, 10 Dec 2021 16:47:51: #2 finished! INFO @ Fri, 10 Dec 2021 16:47:51: #2 predicted fragment length is 165 bps INFO @ Fri, 10 Dec 2021 16:47:51: #2 alternative fragment length(s) may be 165 bps INFO @ Fri, 10 Dec 2021 16:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.10_model.r INFO @ Fri, 10 Dec 2021 16:47:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:47:53: 30000000 INFO @ Fri, 10 Dec 2021 16:47:56: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:47:56: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:47:56: #1 total tags in treatment: 13080355 INFO @ Fri, 10 Dec 2021 16:47:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:47:56: #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 16:47:56: #1 tags after filtering in treatment: 11673899 INFO @ Fri, 10 Dec 2021 16:47:56: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 16:47:56: #1 finished! INFO @ Fri, 10 Dec 2021 16:47:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:47:57: #2 number of paired peaks: 1010 INFO @ Fri, 10 Dec 2021 16:47:57: start model_add_line... INFO @ Fri, 10 Dec 2021 16:47:57: start X-correlation... INFO @ Fri, 10 Dec 2021 16:47:57: end of X-cor INFO @ Fri, 10 Dec 2021 16:47:57: #2 finished! INFO @ Fri, 10 Dec 2021 16:47:57: #2 predicted fragment length is 165 bps INFO @ Fri, 10 Dec 2021 16:47:57: #2 alternative fragment length(s) may be 165 bps INFO @ Fri, 10 Dec 2021 16:47:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.20_model.r INFO @ Fri, 10 Dec 2021 16:47:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:48:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:48:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.10_summits.bed INFO @ Fri, 10 Dec 2021 16:48:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5496 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978931/ERX3978931.20_summits.bed INFO @ Fri, 10 Dec 2021 16:48:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2452 records, 4 fields): 4 millis CompletedMACS2peakCalling