Job ID = 14168654 SRX = ERX3978759 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21333790 spots for ERR3975774/ERR3975774.sra Written 21333790 spots for ERR3975774/ERR3975774.sra Read 12611825 spots for ERR3975782/ERR3975782.sra Written 12611825 spots for ERR3975782/ERR3975782.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169823 ("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: 00:49:38 33945615 reads; of these: 33945615 (100.00%) were paired; of these: 12810589 (37.74%) aligned concordantly 0 times 3255790 (9.59%) aligned concordantly exactly 1 time 17879236 (52.67%) aligned concordantly >1 times ---- 12810589 pairs aligned concordantly 0 times; of these: 881001 (6.88%) aligned discordantly 1 time ---- 11929588 pairs aligned 0 times concordantly or discordantly; of these: 23859176 mates make up the pairs; of these: 10989433 (46.06%) aligned 0 times 406770 (1.70%) aligned exactly 1 time 12462973 (52.24%) aligned >1 times 83.81% overall alignment rate Time searching: 00:49:38 Overall time: 00:49:38 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 40 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] 15891589 / 21762950 = 0.7302 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 20:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.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 20:14:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:14:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:14:38: 1000000 INFO @ Fri, 10 Dec 2021 20:14:47: 2000000 INFO @ Fri, 10 Dec 2021 20:14:56: 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 20:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.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 20:14:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:14:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:15:06: 4000000 INFO @ Fri, 10 Dec 2021 20:15:09: 1000000 INFO @ Fri, 10 Dec 2021 20:15:16: 5000000 INFO @ Fri, 10 Dec 2021 20:15:19: 2000000 INFO @ Fri, 10 Dec 2021 20:15:25: 6000000 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 20:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.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 20:15:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:15:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:15:29: 3000000 INFO @ Fri, 10 Dec 2021 20:15:36: 7000000 INFO @ Fri, 10 Dec 2021 20:15:37: 1000000 INFO @ Fri, 10 Dec 2021 20:15:39: 4000000 INFO @ Fri, 10 Dec 2021 20:15:45: 8000000 INFO @ Fri, 10 Dec 2021 20:15:46: 2000000 INFO @ Fri, 10 Dec 2021 20:15:50: 5000000 INFO @ Fri, 10 Dec 2021 20:15:54: 3000000 INFO @ Fri, 10 Dec 2021 20:15:55: 9000000 INFO @ Fri, 10 Dec 2021 20:16:00: 6000000 INFO @ Fri, 10 Dec 2021 20:16:03: 4000000 INFO @ Fri, 10 Dec 2021 20:16:04: 10000000 INFO @ Fri, 10 Dec 2021 20:16:10: 7000000 INFO @ Fri, 10 Dec 2021 20:16:12: 5000000 INFO @ Fri, 10 Dec 2021 20:16:13: 11000000 INFO @ Fri, 10 Dec 2021 20:16:20: 8000000 INFO @ Fri, 10 Dec 2021 20:16:21: 6000000 INFO @ Fri, 10 Dec 2021 20:16:23: 12000000 INFO @ Fri, 10 Dec 2021 20:16:29: 9000000 INFO @ Fri, 10 Dec 2021 20:16:29: 7000000 INFO @ Fri, 10 Dec 2021 20:16:32: 13000000 INFO @ Fri, 10 Dec 2021 20:16:38: 8000000 INFO @ Fri, 10 Dec 2021 20:16:39: 10000000 INFO @ Fri, 10 Dec 2021 20:16:41: 14000000 INFO @ Fri, 10 Dec 2021 20:16:46: 9000000 INFO @ Fri, 10 Dec 2021 20:16:48: 11000000 INFO @ Fri, 10 Dec 2021 20:16:51: 15000000 INFO @ Fri, 10 Dec 2021 20:16:54: 10000000 INFO @ Fri, 10 Dec 2021 20:16:58: 12000000 INFO @ Fri, 10 Dec 2021 20:17:00: 16000000 INFO @ Fri, 10 Dec 2021 20:17:02: 11000000 INFO @ Fri, 10 Dec 2021 20:17:07: 13000000 INFO @ Fri, 10 Dec 2021 20:17:10: 17000000 INFO @ Fri, 10 Dec 2021 20:17:10: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:17:17: 14000000 INFO @ Fri, 10 Dec 2021 20:17:18: 13000000 INFO @ Fri, 10 Dec 2021 20:17:19: 18000000 INFO @ Fri, 10 Dec 2021 20:17:26: 15000000 INFO @ Fri, 10 Dec 2021 20:17:26: 14000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:17:29: 19000000 INFO @ Fri, 10 Dec 2021 20:17:35: 15000000 INFO @ Fri, 10 Dec 2021 20:17:36: 16000000 INFO @ Fri, 10 Dec 2021 20:17:38: 20000000 INFO @ Fri, 10 Dec 2021 20:17:43: 16000000 INFO @ Fri, 10 Dec 2021 20:17:46: 17000000 INFO @ Fri, 10 Dec 2021 20:17:48: 21000000 INFO @ Fri, 10 Dec 2021 20:17:51: 17000000 INFO @ Fri, 10 Dec 2021 20:17:55: 18000000 INFO @ Fri, 10 Dec 2021 20:17:57: 22000000 INFO @ Fri, 10 Dec 2021 20:18:00: 18000000 INFO @ Fri, 10 Dec 2021 20:18:05: 19000000 INFO @ Fri, 10 Dec 2021 20:18:07: 23000000 INFO @ Fri, 10 Dec 2021 20:18:08: 19000000 INFO @ Fri, 10 Dec 2021 20:18:14: 20000000 INFO @ Fri, 10 Dec 2021 20:18:17: 20000000 INFO @ Fri, 10 Dec 2021 20:18:17: 24000000 INFO @ Fri, 10 Dec 2021 20:18:24: 21000000 INFO @ Fri, 10 Dec 2021 20:18:25: 21000000 INFO @ Fri, 10 Dec 2021 20:18:27: 25000000 INFO @ Fri, 10 Dec 2021 20:18:28: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:18:28: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:18:28: #1 total tags in treatment: 5381484 INFO @ Fri, 10 Dec 2021 20:18:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:18:28: #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 20:18:28: #1 tags after filtering in treatment: 3359064 INFO @ Fri, 10 Dec 2021 20:18:28: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 10 Dec 2021 20:18:28: #1 finished! INFO @ Fri, 10 Dec 2021 20:18:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:18:29: #2 number of paired peaks: 4027 INFO @ Fri, 10 Dec 2021 20:18:29: start model_add_line... INFO @ Fri, 10 Dec 2021 20:18:29: start X-correlation... INFO @ Fri, 10 Dec 2021 20:18:29: end of X-cor INFO @ Fri, 10 Dec 2021 20:18:29: #2 finished! INFO @ Fri, 10 Dec 2021 20:18:29: #2 predicted fragment length is 194 bps INFO @ Fri, 10 Dec 2021 20:18:29: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 10 Dec 2021 20:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.05_model.r WARNING @ Fri, 10 Dec 2021 20:18:29: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:18:29: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Fri, 10 Dec 2021 20:18:29: #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 20:18:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:18:33: 22000000 INFO @ Fri, 10 Dec 2021 20:18:35: 22000000 INFO @ Fri, 10 Dec 2021 20:18:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.05_summits.bed INFO @ Fri, 10 Dec 2021 20:18:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7185 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:18:43: 23000000 INFO @ Fri, 10 Dec 2021 20:18:44: 23000000 INFO @ Fri, 10 Dec 2021 20:18:53: 24000000 INFO @ Fri, 10 Dec 2021 20:18:54: 24000000 INFO @ Fri, 10 Dec 2021 20:19:04: 25000000 INFO @ Fri, 10 Dec 2021 20:19:04: 25000000 INFO @ Fri, 10 Dec 2021 20:19:05: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:19:05: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:19:05: #1 total tags in treatment: 5381484 INFO @ Fri, 10 Dec 2021 20:19:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:19:05: #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 20:19:05: #1 tags after filtering in treatment: 3359064 INFO @ Fri, 10 Dec 2021 20:19:05: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 10 Dec 2021 20:19:05: #1 finished! INFO @ Fri, 10 Dec 2021 20:19:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:19:05: #2 number of paired peaks: 4027 INFO @ Fri, 10 Dec 2021 20:19:05: start model_add_line... INFO @ Fri, 10 Dec 2021 20:19:05: start X-correlation... INFO @ Fri, 10 Dec 2021 20:19:05: end of X-cor INFO @ Fri, 10 Dec 2021 20:19:05: #2 finished! INFO @ Fri, 10 Dec 2021 20:19:05: #2 predicted fragment length is 194 bps INFO @ Fri, 10 Dec 2021 20:19:05: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 10 Dec 2021 20:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.10_model.r WARNING @ Fri, 10 Dec 2021 20:19:05: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:19:05: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Fri, 10 Dec 2021 20:19:05: #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 20:19:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:19:05: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:19:05: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:19:05: #1 total tags in treatment: 5381484 INFO @ Fri, 10 Dec 2021 20:19:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:19:05: #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 20:19:05: #1 tags after filtering in treatment: 3359064 INFO @ Fri, 10 Dec 2021 20:19:05: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 10 Dec 2021 20:19:05: #1 finished! INFO @ Fri, 10 Dec 2021 20:19:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:19:06: #2 number of paired peaks: 4027 INFO @ Fri, 10 Dec 2021 20:19:06: start model_add_line... INFO @ Fri, 10 Dec 2021 20:19:06: start X-correlation... INFO @ Fri, 10 Dec 2021 20:19:06: end of X-cor INFO @ Fri, 10 Dec 2021 20:19:06: #2 finished! INFO @ Fri, 10 Dec 2021 20:19:06: #2 predicted fragment length is 194 bps INFO @ Fri, 10 Dec 2021 20:19:06: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 10 Dec 2021 20:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.20_model.r WARNING @ Fri, 10 Dec 2021 20:19:06: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:19:06: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Fri, 10 Dec 2021 20:19:06: #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 20:19:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:19:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:19:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.10_summits.bed INFO @ Fri, 10 Dec 2021 20:19:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3593 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978759/ERX3978759.20_summits.bed INFO @ Fri, 10 Dec 2021 20:19:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1138 records, 4 fields): 4 millis CompletedMACS2peakCalling