Job ID = 14168712 SRX = ERX3978767 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25109491 spots for ERR3975783/ERR3975783.sra Written 25109491 spots for ERR3975783/ERR3975783.sra Read 19927888 spots for ERR3975810/ERR3975810.sra Written 19927888 spots for ERR3975810/ERR3975810.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169870 ("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: 01:04:02 45037379 reads; of these: 45037379 (100.00%) were paired; of these: 13314038 (29.56%) aligned concordantly 0 times 3578005 (7.94%) aligned concordantly exactly 1 time 28145336 (62.49%) aligned concordantly >1 times ---- 13314038 pairs aligned concordantly 0 times; of these: 1143868 (8.59%) aligned discordantly 1 time ---- 12170170 pairs aligned 0 times concordantly or discordantly; of these: 24340340 mates make up the pairs; of these: 10189280 (41.86%) aligned 0 times 422382 (1.74%) aligned exactly 1 time 13728678 (56.40%) aligned >1 times 88.69% overall alignment rate Time searching: 01:04:02 Overall time: 01:04:02 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 56 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] 25698312 / 32581932 = 0.7887 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 21:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.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 21:08:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:08:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:08:12: 1000000 INFO @ Fri, 10 Dec 2021 21:08:23: 2000000 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 21:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.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 21:08:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:08:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:08:34: 3000000 INFO @ Fri, 10 Dec 2021 21:08:43: 1000000 INFO @ Fri, 10 Dec 2021 21:08:46: 4000000 INFO @ Fri, 10 Dec 2021 21:08:55: 2000000 INFO @ Fri, 10 Dec 2021 21:08:57: 5000000 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 21:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.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 21:09:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:09:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:09:07: 3000000 INFO @ Fri, 10 Dec 2021 21:09:09: 6000000 INFO @ Fri, 10 Dec 2021 21:09:13: 1000000 INFO @ Fri, 10 Dec 2021 21:09:20: 4000000 INFO @ Fri, 10 Dec 2021 21:09:21: 7000000 INFO @ Fri, 10 Dec 2021 21:09:25: 2000000 INFO @ Fri, 10 Dec 2021 21:09:32: 5000000 INFO @ Fri, 10 Dec 2021 21:09:33: 8000000 INFO @ Fri, 10 Dec 2021 21:09:38: 3000000 INFO @ Fri, 10 Dec 2021 21:09:44: 6000000 INFO @ Fri, 10 Dec 2021 21:09:44: 9000000 INFO @ Fri, 10 Dec 2021 21:09:50: 4000000 INFO @ Fri, 10 Dec 2021 21:09:56: 10000000 INFO @ Fri, 10 Dec 2021 21:09:56: 7000000 INFO @ Fri, 10 Dec 2021 21:10:02: 5000000 INFO @ Fri, 10 Dec 2021 21:10:07: 11000000 INFO @ Fri, 10 Dec 2021 21:10:08: 8000000 INFO @ Fri, 10 Dec 2021 21:10:14: 6000000 INFO @ Fri, 10 Dec 2021 21:10:19: 12000000 INFO @ Fri, 10 Dec 2021 21:10:20: 9000000 INFO @ Fri, 10 Dec 2021 21:10:26: 7000000 INFO @ Fri, 10 Dec 2021 21:10:30: 13000000 INFO @ Fri, 10 Dec 2021 21:10:32: 10000000 INFO @ Fri, 10 Dec 2021 21:10:38: 8000000 INFO @ Fri, 10 Dec 2021 21:10:41: 14000000 INFO @ Fri, 10 Dec 2021 21:10:43: 11000000 INFO @ Fri, 10 Dec 2021 21:10:49: 9000000 INFO @ Fri, 10 Dec 2021 21:10:52: 15000000 INFO @ Fri, 10 Dec 2021 21:10:55: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:11:00: 10000000 INFO @ Fri, 10 Dec 2021 21:11:04: 16000000 INFO @ Fri, 10 Dec 2021 21:11:07: 13000000 INFO @ Fri, 10 Dec 2021 21:11:11: 11000000 INFO @ Fri, 10 Dec 2021 21:11:15: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:11:18: 14000000 INFO @ Fri, 10 Dec 2021 21:11:22: 12000000 INFO @ Fri, 10 Dec 2021 21:11:26: 18000000 INFO @ Fri, 10 Dec 2021 21:11:30: 15000000 INFO @ Fri, 10 Dec 2021 21:11:33: 13000000 INFO @ Fri, 10 Dec 2021 21:11:37: 19000000 INFO @ Fri, 10 Dec 2021 21:11:42: 16000000 INFO @ Fri, 10 Dec 2021 21:11:43: 14000000 INFO @ Fri, 10 Dec 2021 21:11:48: 20000000 INFO @ Fri, 10 Dec 2021 21:11:54: 17000000 INFO @ Fri, 10 Dec 2021 21:11:54: 15000000 INFO @ Fri, 10 Dec 2021 21:12:00: 21000000 INFO @ Fri, 10 Dec 2021 21:12:05: 16000000 INFO @ Fri, 10 Dec 2021 21:12:05: 18000000 INFO @ Fri, 10 Dec 2021 21:12:11: 22000000 INFO @ Fri, 10 Dec 2021 21:12:16: 17000000 INFO @ Fri, 10 Dec 2021 21:12:17: 19000000 INFO @ Fri, 10 Dec 2021 21:12:22: 23000000 INFO @ Fri, 10 Dec 2021 21:12:27: 18000000 INFO @ Fri, 10 Dec 2021 21:12:29: 20000000 INFO @ Fri, 10 Dec 2021 21:12:33: 24000000 INFO @ Fri, 10 Dec 2021 21:12:38: 19000000 INFO @ Fri, 10 Dec 2021 21:12:41: 21000000 INFO @ Fri, 10 Dec 2021 21:12:44: 25000000 INFO @ Fri, 10 Dec 2021 21:12:49: 20000000 INFO @ Fri, 10 Dec 2021 21:12:52: 22000000 INFO @ Fri, 10 Dec 2021 21:12:56: 26000000 INFO @ Fri, 10 Dec 2021 21:12:59: 21000000 INFO @ Fri, 10 Dec 2021 21:13:04: 23000000 INFO @ Fri, 10 Dec 2021 21:13:08: 27000000 INFO @ Fri, 10 Dec 2021 21:13:10: 22000000 INFO @ Fri, 10 Dec 2021 21:13:16: 24000000 INFO @ Fri, 10 Dec 2021 21:13:19: 28000000 INFO @ Fri, 10 Dec 2021 21:13:21: 23000000 INFO @ Fri, 10 Dec 2021 21:13:25: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:13:25: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:13:25: #1 total tags in treatment: 6203952 INFO @ Fri, 10 Dec 2021 21:13:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:13:25: #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 21:13:25: #1 tags after filtering in treatment: 3536313 INFO @ Fri, 10 Dec 2021 21:13:25: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Dec 2021 21:13:25: #1 finished! INFO @ Fri, 10 Dec 2021 21:13:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:13:25: #2 number of paired peaks: 4046 INFO @ Fri, 10 Dec 2021 21:13:25: start model_add_line... INFO @ Fri, 10 Dec 2021 21:13:25: start X-correlation... INFO @ Fri, 10 Dec 2021 21:13:25: end of X-cor INFO @ Fri, 10 Dec 2021 21:13:25: #2 finished! INFO @ Fri, 10 Dec 2021 21:13:25: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 21:13:25: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 21:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.05_model.r WARNING @ Fri, 10 Dec 2021 21:13:25: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:13:25: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Fri, 10 Dec 2021 21:13:25: #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 21:13:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:13:27: 25000000 INFO @ Fri, 10 Dec 2021 21:13:32: 24000000 INFO @ Fri, 10 Dec 2021 21:13:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.05_summits.bed INFO @ Fri, 10 Dec 2021 21:13:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7466 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:13:38: 26000000 INFO @ Fri, 10 Dec 2021 21:13:42: 25000000 INFO @ Fri, 10 Dec 2021 21:13:49: 27000000 INFO @ Fri, 10 Dec 2021 21:13:53: 26000000 INFO @ Fri, 10 Dec 2021 21:14:00: 28000000 INFO @ Fri, 10 Dec 2021 21:14:04: 27000000 INFO @ Fri, 10 Dec 2021 21:14:06: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:14:06: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:14:06: #1 total tags in treatment: 6203952 INFO @ Fri, 10 Dec 2021 21:14:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:14:06: #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 21:14:06: #1 tags after filtering in treatment: 3536313 INFO @ Fri, 10 Dec 2021 21:14:06: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Dec 2021 21:14:06: #1 finished! INFO @ Fri, 10 Dec 2021 21:14:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:14:06: #2 number of paired peaks: 4046 INFO @ Fri, 10 Dec 2021 21:14:06: start model_add_line... INFO @ Fri, 10 Dec 2021 21:14:06: start X-correlation... INFO @ Fri, 10 Dec 2021 21:14:06: end of X-cor INFO @ Fri, 10 Dec 2021 21:14:06: #2 finished! INFO @ Fri, 10 Dec 2021 21:14:06: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 21:14:06: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 21:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.10_model.r WARNING @ Fri, 10 Dec 2021 21:14:06: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:14:06: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Fri, 10 Dec 2021 21:14:06: #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 21:14:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:14:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:14:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:14:14: 28000000 INFO @ Fri, 10 Dec 2021 21:14:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:14:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:14:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.10_summits.bed INFO @ Fri, 10 Dec 2021 21:14:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3964 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:14:19: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:14:19: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:14:19: #1 total tags in treatment: 6203952 INFO @ Fri, 10 Dec 2021 21:14:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:14:19: #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 21:14:19: #1 tags after filtering in treatment: 3536313 INFO @ Fri, 10 Dec 2021 21:14:19: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Dec 2021 21:14:19: #1 finished! INFO @ Fri, 10 Dec 2021 21:14:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:14:20: #2 number of paired peaks: 4046 INFO @ Fri, 10 Dec 2021 21:14:20: start model_add_line... INFO @ Fri, 10 Dec 2021 21:14:20: start X-correlation... INFO @ Fri, 10 Dec 2021 21:14:20: end of X-cor INFO @ Fri, 10 Dec 2021 21:14:20: #2 finished! INFO @ Fri, 10 Dec 2021 21:14:20: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 21:14:20: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 21:14:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.20_model.r WARNING @ Fri, 10 Dec 2021 21:14:20: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:14:20: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Fri, 10 Dec 2021 21:14:20: #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 21:14:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:14:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978767/ERX3978767.20_summits.bed INFO @ Fri, 10 Dec 2021 21:14:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 3 millis CompletedMACS2peakCalling