Job ID = 14169015 SRX = ERX3978781 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24780881 spots for ERR3975803/ERR3975803.sra Written 24780881 spots for ERR3975803/ERR3975803.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170274 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:03:40 24780881 reads; of these: 24780881 (100.00%) were paired; of these: 9295063 (37.51%) aligned concordantly 0 times 5382314 (21.72%) aligned concordantly exactly 1 time 10103504 (40.77%) aligned concordantly >1 times ---- 9295063 pairs aligned concordantly 0 times; of these: 1891589 (20.35%) aligned discordantly 1 time ---- 7403474 pairs aligned 0 times concordantly or discordantly; of these: 14806948 mates make up the pairs; of these: 8627285 (58.27%) aligned 0 times 389480 (2.63%) aligned exactly 1 time 5790183 (39.10%) aligned >1 times 82.59% overall alignment rate Time searching: 01:03:41 Overall time: 01:03:41 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 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] 8366816 / 17245336 = 0.4852 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 @ Sat, 11 Dec 2021 00:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.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 @ Sat, 11 Dec 2021 00:21:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:21:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:21:26: 1000000 INFO @ Sat, 11 Dec 2021 00:21:33: 2000000 INFO @ Sat, 11 Dec 2021 00:21:41: 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 @ Sat, 11 Dec 2021 00:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.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 @ Sat, 11 Dec 2021 00:21:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:21:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:21:48: 4000000 INFO @ Sat, 11 Dec 2021 00:21:56: 1000000 INFO @ Sat, 11 Dec 2021 00:21:57: 5000000 INFO @ Sat, 11 Dec 2021 00:22:05: 6000000 INFO @ Sat, 11 Dec 2021 00:22:05: 2000000 INFO @ Sat, 11 Dec 2021 00:22:13: 7000000 INFO @ Sat, 11 Dec 2021 00:22:13: 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 @ Sat, 11 Dec 2021 00:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.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 @ Sat, 11 Dec 2021 00:22:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:22:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:22:21: 4000000 INFO @ Sat, 11 Dec 2021 00:22:21: 8000000 INFO @ Sat, 11 Dec 2021 00:22:25: 1000000 INFO @ Sat, 11 Dec 2021 00:22:30: 5000000 INFO @ Sat, 11 Dec 2021 00:22:30: 9000000 INFO @ Sat, 11 Dec 2021 00:22:34: 2000000 INFO @ Sat, 11 Dec 2021 00:22:38: 6000000 INFO @ Sat, 11 Dec 2021 00:22:39: 10000000 INFO @ Sat, 11 Dec 2021 00:22:42: 3000000 INFO @ Sat, 11 Dec 2021 00:22:47: 7000000 INFO @ Sat, 11 Dec 2021 00:22:48: 11000000 INFO @ Sat, 11 Dec 2021 00:22:51: 4000000 INFO @ Sat, 11 Dec 2021 00:22:55: 8000000 INFO @ Sat, 11 Dec 2021 00:22:56: 12000000 INFO @ Sat, 11 Dec 2021 00:23:00: 5000000 INFO @ Sat, 11 Dec 2021 00:23:04: 9000000 INFO @ Sat, 11 Dec 2021 00:23:04: 13000000 INFO @ Sat, 11 Dec 2021 00:23:08: 6000000 INFO @ Sat, 11 Dec 2021 00:23:11: 14000000 INFO @ Sat, 11 Dec 2021 00:23:12: 10000000 INFO @ Sat, 11 Dec 2021 00:23:17: 7000000 INFO @ Sat, 11 Dec 2021 00:23:19: 15000000 INFO @ Sat, 11 Dec 2021 00:23:21: 11000000 INFO @ Sat, 11 Dec 2021 00:23:26: 8000000 INFO @ Sat, 11 Dec 2021 00:23:27: 16000000 INFO @ Sat, 11 Dec 2021 00:23:30: 12000000 INFO @ Sat, 11 Dec 2021 00:23:34: 9000000 INFO @ Sat, 11 Dec 2021 00:23:35: 17000000 INFO @ Sat, 11 Dec 2021 00:23:38: 13000000 INFO @ Sat, 11 Dec 2021 00:23:42: 18000000 INFO @ Sat, 11 Dec 2021 00:23:42: 10000000 INFO @ Sat, 11 Dec 2021 00:23:45: 14000000 INFO @ Sat, 11 Dec 2021 00:23:51: 19000000 INFO @ Sat, 11 Dec 2021 00:23:51: 11000000 INFO @ Sat, 11 Dec 2021 00:23:53: 15000000 INFO @ Sat, 11 Dec 2021 00:24:00: 20000000 INFO @ Sat, 11 Dec 2021 00:24:00: 12000000 INFO @ Sat, 11 Dec 2021 00:24:01: 16000000 INFO @ Sat, 11 Dec 2021 00:24:08: 13000000 INFO @ Sat, 11 Dec 2021 00:24:09: 17000000 INFO @ Sat, 11 Dec 2021 00:24:09: 21000000 INFO @ Sat, 11 Dec 2021 00:24:15: 14000000 INFO @ Sat, 11 Dec 2021 00:24:16: 18000000 INFO @ Sat, 11 Dec 2021 00:24:18: 22000000 INFO @ Sat, 11 Dec 2021 00:24:24: 15000000 INFO @ Sat, 11 Dec 2021 00:24:24: 19000000 INFO @ Sat, 11 Dec 2021 00:24:27: 23000000 INFO @ Sat, 11 Dec 2021 00:24:31: 16000000 INFO @ Sat, 11 Dec 2021 00:24:31: 20000000 INFO @ Sat, 11 Dec 2021 00:24:36: 24000000 INFO @ Sat, 11 Dec 2021 00:24:37: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 00:24:37: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 00:24:37: #1 total tags in treatment: 7253337 INFO @ Sat, 11 Dec 2021 00:24:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:24:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 00:24:37: #1 tags after filtering in treatment: 5082881 INFO @ Sat, 11 Dec 2021 00:24:37: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 00:24:37: #1 finished! INFO @ Sat, 11 Dec 2021 00:24:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:24:38: #2 number of paired peaks: 3197 INFO @ Sat, 11 Dec 2021 00:24:38: start model_add_line... INFO @ Sat, 11 Dec 2021 00:24:38: start X-correlation... INFO @ Sat, 11 Dec 2021 00:24:38: end of X-cor INFO @ Sat, 11 Dec 2021 00:24:38: #2 finished! INFO @ Sat, 11 Dec 2021 00:24:38: #2 predicted fragment length is 212 bps INFO @ Sat, 11 Dec 2021 00:24:38: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 11 Dec 2021 00:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.05_model.r WARNING @ Sat, 11 Dec 2021 00:24:38: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:24:38: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 11 Dec 2021 00:24:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:24:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:24:39: 17000000 INFO @ Sat, 11 Dec 2021 00:24:39: 21000000 INFO @ Sat, 11 Dec 2021 00:24:46: 18000000 INFO @ Sat, 11 Dec 2021 00:24:47: 22000000 INFO @ Sat, 11 Dec 2021 00:24:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:24:54: 19000000 INFO @ Sat, 11 Dec 2021 00:24:55: 23000000 INFO @ Sat, 11 Dec 2021 00:24:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:24:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:24:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.05_summits.bed INFO @ Sat, 11 Dec 2021 00:24:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9497 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:25:02: 20000000 INFO @ Sat, 11 Dec 2021 00:25:03: 24000000 INFO @ Sat, 11 Dec 2021 00:25:04: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 00:25:04: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 00:25:04: #1 total tags in treatment: 7253337 INFO @ Sat, 11 Dec 2021 00:25:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:25:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 00:25:04: #1 tags after filtering in treatment: 5082881 INFO @ Sat, 11 Dec 2021 00:25:04: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 00:25:04: #1 finished! INFO @ Sat, 11 Dec 2021 00:25:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:25:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:25:05: #2 number of paired peaks: 3197 INFO @ Sat, 11 Dec 2021 00:25:05: start model_add_line... INFO @ Sat, 11 Dec 2021 00:25:05: start X-correlation... INFO @ Sat, 11 Dec 2021 00:25:05: end of X-cor INFO @ Sat, 11 Dec 2021 00:25:05: #2 finished! INFO @ Sat, 11 Dec 2021 00:25:05: #2 predicted fragment length is 212 bps INFO @ Sat, 11 Dec 2021 00:25:05: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 11 Dec 2021 00:25:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.10_model.r WARNING @ Sat, 11 Dec 2021 00:25:05: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:25:05: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 11 Dec 2021 00:25:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:25:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:25:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:25:10: 21000000 INFO @ Sat, 11 Dec 2021 00:25:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:25:18: 22000000 INFO @ Sat, 11 Dec 2021 00:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.10_summits.bed INFO @ Sat, 11 Dec 2021 00:25:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5198 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:25:26: 23000000 INFO @ Sat, 11 Dec 2021 00:25:34: 24000000 INFO @ Sat, 11 Dec 2021 00:25:36: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 00:25:36: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 00:25:36: #1 total tags in treatment: 7253337 INFO @ Sat, 11 Dec 2021 00:25:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:25:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 00:25:36: #1 tags after filtering in treatment: 5082881 INFO @ Sat, 11 Dec 2021 00:25:36: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 00:25:36: #1 finished! INFO @ Sat, 11 Dec 2021 00:25:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:25:37: #2 number of paired peaks: 3197 INFO @ Sat, 11 Dec 2021 00:25:37: start model_add_line... INFO @ Sat, 11 Dec 2021 00:25:37: start X-correlation... INFO @ Sat, 11 Dec 2021 00:25:37: end of X-cor INFO @ Sat, 11 Dec 2021 00:25:37: #2 finished! INFO @ Sat, 11 Dec 2021 00:25:37: #2 predicted fragment length is 212 bps INFO @ Sat, 11 Dec 2021 00:25:37: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 11 Dec 2021 00:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.20_model.r WARNING @ Sat, 11 Dec 2021 00:25:37: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:25:37: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Sat, 11 Dec 2021 00:25:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:25:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:25:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:25:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978781/ERX3978781.20_summits.bed INFO @ Sat, 11 Dec 2021 00:25:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1743 records, 4 fields): 5 millis CompletedMACS2peakCalling