Job ID = 14168703 SRX = ERX3978764 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18384346 spots for ERR3975779/ERR3975779.sra Written 18384346 spots for ERR3975779/ERR3975779.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169828 ("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: 00:38:02 18384346 reads; of these: 18384346 (100.00%) were paired; of these: 7133336 (38.80%) aligned concordantly 0 times 6484469 (35.27%) aligned concordantly exactly 1 time 4766541 (25.93%) aligned concordantly >1 times ---- 7133336 pairs aligned concordantly 0 times; of these: 2275324 (31.90%) aligned discordantly 1 time ---- 4858012 pairs aligned 0 times concordantly or discordantly; of these: 9716024 mates make up the pairs; of these: 6113537 (62.92%) aligned 0 times 381865 (3.93%) aligned exactly 1 time 3220622 (33.15%) aligned >1 times 83.37% overall alignment rate Time searching: 00:38:02 Overall time: 00:38:02 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 20 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] 3521278 / 13443864 = 0.2619 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 20:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.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 20:15:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:15:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:15:26: 1000000 INFO @ Fri, 10 Dec 2021 20:15:33: 2000000 INFO @ Fri, 10 Dec 2021 20:15:40: 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 20:15:47: 4000000 INFO @ Fri, 10 Dec 2021 20:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.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 20:15:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:15:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:15:55: 5000000 INFO @ Fri, 10 Dec 2021 20:15:56: 1000000 INFO @ Fri, 10 Dec 2021 20:16:03: 6000000 INFO @ Fri, 10 Dec 2021 20:16:05: 2000000 INFO @ Fri, 10 Dec 2021 20:16:12: 7000000 INFO @ Fri, 10 Dec 2021 20:16:13: 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 @ Fri, 10 Dec 2021 20:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.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 20:16:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:16:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:16:20: 8000000 INFO @ Fri, 10 Dec 2021 20:16:22: 4000000 INFO @ Fri, 10 Dec 2021 20:16:26: 1000000 INFO @ Fri, 10 Dec 2021 20:16:29: 9000000 INFO @ Fri, 10 Dec 2021 20:16:30: 5000000 INFO @ Fri, 10 Dec 2021 20:16:35: 2000000 INFO @ Fri, 10 Dec 2021 20:16:37: 10000000 INFO @ Fri, 10 Dec 2021 20:16:39: 6000000 INFO @ Fri, 10 Dec 2021 20:16:43: 3000000 INFO @ Fri, 10 Dec 2021 20:16:46: 11000000 INFO @ Fri, 10 Dec 2021 20:16:48: 7000000 INFO @ Fri, 10 Dec 2021 20:16:52: 4000000 INFO @ Fri, 10 Dec 2021 20:16:54: 12000000 INFO @ Fri, 10 Dec 2021 20:16:56: 8000000 INFO @ Fri, 10 Dec 2021 20:17:00: 5000000 INFO @ Fri, 10 Dec 2021 20:17:03: 13000000 INFO @ Fri, 10 Dec 2021 20:17:05: 9000000 INFO @ Fri, 10 Dec 2021 20:17:09: 6000000 INFO @ Fri, 10 Dec 2021 20:17:11: 14000000 INFO @ Fri, 10 Dec 2021 20:17:13: 10000000 INFO @ Fri, 10 Dec 2021 20:17:17: 7000000 INFO @ Fri, 10 Dec 2021 20:17:20: 15000000 INFO @ Fri, 10 Dec 2021 20:17:22: 11000000 INFO @ Fri, 10 Dec 2021 20:17:26: 8000000 INFO @ Fri, 10 Dec 2021 20:17:28: 16000000 INFO @ Fri, 10 Dec 2021 20:17:30: 12000000 INFO @ Fri, 10 Dec 2021 20:17:34: 9000000 INFO @ Fri, 10 Dec 2021 20:17:36: 17000000 INFO @ Fri, 10 Dec 2021 20:17:39: 13000000 INFO @ Fri, 10 Dec 2021 20:17:42: 10000000 INFO @ Fri, 10 Dec 2021 20:17:45: 18000000 INFO @ Fri, 10 Dec 2021 20:17:47: 14000000 INFO @ Fri, 10 Dec 2021 20:17:51: 11000000 INFO @ Fri, 10 Dec 2021 20:17:53: 19000000 INFO @ Fri, 10 Dec 2021 20:17:56: 15000000 INFO @ Fri, 10 Dec 2021 20:17:59: 12000000 INFO @ Fri, 10 Dec 2021 20:18:01: 20000000 INFO @ Fri, 10 Dec 2021 20:18:04: 16000000 INFO @ Fri, 10 Dec 2021 20:18:08: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:18:10: 21000000 INFO @ Fri, 10 Dec 2021 20:18:12: 17000000 INFO @ Fri, 10 Dec 2021 20:18:16: 14000000 INFO @ Fri, 10 Dec 2021 20:18:18: 22000000 INFO @ Fri, 10 Dec 2021 20:18:20: 18000000 INFO @ Fri, 10 Dec 2021 20:18:24: 15000000 INFO @ Fri, 10 Dec 2021 20:18:27: 23000000 INFO @ Fri, 10 Dec 2021 20:18:28: 19000000 INFO @ Fri, 10 Dec 2021 20:18:32: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:18:32: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:18:32: #1 total tags in treatment: 7861262 INFO @ Fri, 10 Dec 2021 20:18:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:18:32: #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 20:18:32: #1 tags after filtering in treatment: 5688581 INFO @ Fri, 10 Dec 2021 20:18:32: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 20:18:32: #1 finished! INFO @ Fri, 10 Dec 2021 20:18:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:18:32: 16000000 INFO @ Fri, 10 Dec 2021 20:18:33: #2 number of paired peaks: 5140 INFO @ Fri, 10 Dec 2021 20:18:33: start model_add_line... INFO @ Fri, 10 Dec 2021 20:18:33: start X-correlation... INFO @ Fri, 10 Dec 2021 20:18:33: end of X-cor INFO @ Fri, 10 Dec 2021 20:18:33: #2 finished! INFO @ Fri, 10 Dec 2021 20:18:33: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 20:18:33: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 20:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.05_model.r WARNING @ Fri, 10 Dec 2021 20:18:33: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:18:33: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 20:18:33: #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 20:18:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:18:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:18:37: 20000000 INFO @ Fri, 10 Dec 2021 20:18:40: 17000000 INFO @ Fri, 10 Dec 2021 20:18:45: 21000000 INFO @ Fri, 10 Dec 2021 20:18:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:18:48: 18000000 INFO @ Fri, 10 Dec 2021 20:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.05_summits.bed INFO @ Fri, 10 Dec 2021 20:18:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10368 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:18:54: 22000000 INFO @ Fri, 10 Dec 2021 20:18:56: 19000000 INFO @ Fri, 10 Dec 2021 20:19:02: 23000000 INFO @ Fri, 10 Dec 2021 20:19:05: 20000000 INFO @ Fri, 10 Dec 2021 20:19:08: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:19:08: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:19:08: #1 total tags in treatment: 7861262 INFO @ Fri, 10 Dec 2021 20:19:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:19:08: #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 20:19:08: #1 tags after filtering in treatment: 5688581 INFO @ Fri, 10 Dec 2021 20:19:08: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 20:19:08: #1 finished! INFO @ Fri, 10 Dec 2021 20:19:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:19:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:19:08: #2 number of paired peaks: 5140 INFO @ Fri, 10 Dec 2021 20:19:08: start model_add_line... INFO @ Fri, 10 Dec 2021 20:19:08: start X-correlation... INFO @ Fri, 10 Dec 2021 20:19:08: end of X-cor INFO @ Fri, 10 Dec 2021 20:19:08: #2 finished! INFO @ Fri, 10 Dec 2021 20:19:08: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 20:19:08: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 20:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.10_model.r WARNING @ Fri, 10 Dec 2021 20:19:08: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:19:08: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 20:19:08: #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 20:19:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:19:13: 21000000 INFO @ Fri, 10 Dec 2021 20:19:20: 22000000 INFO @ Fri, 10 Dec 2021 20:19:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:19:28: 23000000 INFO @ Fri, 10 Dec 2021 20:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.10_summits.bed INFO @ Fri, 10 Dec 2021 20:19:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6722 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:19:33: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:19:33: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:19:33: #1 total tags in treatment: 7861262 INFO @ Fri, 10 Dec 2021 20:19:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:19:33: #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 20:19:33: #1 tags after filtering in treatment: 5688581 INFO @ Fri, 10 Dec 2021 20:19:33: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 20:19:33: #1 finished! INFO @ Fri, 10 Dec 2021 20:19:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:19:33: #2 number of paired peaks: 5140 INFO @ Fri, 10 Dec 2021 20:19:33: start model_add_line... INFO @ Fri, 10 Dec 2021 20:19:33: start X-correlation... INFO @ Fri, 10 Dec 2021 20:19:33: end of X-cor INFO @ Fri, 10 Dec 2021 20:19:33: #2 finished! INFO @ Fri, 10 Dec 2021 20:19:33: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 20:19:33: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 20:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.20_model.r WARNING @ Fri, 10 Dec 2021 20:19:33: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:19:33: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 20:19:33: #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 20:19:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:19:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:19:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978764/ERX3978764.20_summits.bed INFO @ Fri, 10 Dec 2021 20:19:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2805 records, 4 fields): 4 millis CompletedMACS2peakCalling