Job ID = 14168279 SRX = ERX3978848 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27297046 spots for ERR3975917/ERR3975917.sra Written 27297046 spots for ERR3975917/ERR3975917.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169667 ("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: 02:20:02 27297046 reads; of these: 27297046 (100.00%) were paired; of these: 11222128 (41.11%) aligned concordantly 0 times 11922312 (43.68%) aligned concordantly exactly 1 time 4152606 (15.21%) aligned concordantly >1 times ---- 11222128 pairs aligned concordantly 0 times; of these: 757760 (6.75%) aligned discordantly 1 time ---- 10464368 pairs aligned 0 times concordantly or discordantly; of these: 20928736 mates make up the pairs; of these: 9817745 (46.91%) aligned 0 times 6255055 (29.89%) aligned exactly 1 time 4855936 (23.20%) aligned >1 times 82.02% overall alignment rate Time searching: 02:20:02 Overall time: 02:20:02 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] 13155394 / 16527547 = 0.7960 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 19:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.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 19:20:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:20:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:20:38: 1000000 INFO @ Fri, 10 Dec 2021 19:20:43: 2000000 INFO @ Fri, 10 Dec 2021 19:20:49: 3000000 INFO @ Fri, 10 Dec 2021 19:20:55: 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 19:21:00: 5000000 INFO @ Fri, 10 Dec 2021 19:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.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 19:21:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:21:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:21:07: 6000000 INFO @ Fri, 10 Dec 2021 19:21:11: 1000000 INFO @ Fri, 10 Dec 2021 19:21:14: 7000000 INFO @ Fri, 10 Dec 2021 19:21:19: 2000000 INFO @ Fri, 10 Dec 2021 19:21:22: 8000000 INFO @ Fri, 10 Dec 2021 19:21:28: 3000000 INFO @ Fri, 10 Dec 2021 19:21:29: 9000000 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 19:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.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 19:21:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:21:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:21:36: 4000000 INFO @ Fri, 10 Dec 2021 19:21:37: 10000000 INFO @ Fri, 10 Dec 2021 19:21:40: 1000000 INFO @ Fri, 10 Dec 2021 19:21:44: 11000000 INFO @ Fri, 10 Dec 2021 19:21:44: 5000000 INFO @ Fri, 10 Dec 2021 19:21:47: 2000000 INFO @ Fri, 10 Dec 2021 19:21:52: 12000000 INFO @ Fri, 10 Dec 2021 19:21:53: 6000000 INFO @ Fri, 10 Dec 2021 19:21:55: 3000000 INFO @ Fri, 10 Dec 2021 19:21:59: 13000000 INFO @ Fri, 10 Dec 2021 19:22:01: 7000000 INFO @ Fri, 10 Dec 2021 19:22:02: 4000000 INFO @ Fri, 10 Dec 2021 19:22:07: 14000000 INFO @ Fri, 10 Dec 2021 19:22:09: 8000000 INFO @ Fri, 10 Dec 2021 19:22:10: 5000000 INFO @ Fri, 10 Dec 2021 19:22:15: 15000000 INFO @ Fri, 10 Dec 2021 19:22:17: 6000000 INFO @ Fri, 10 Dec 2021 19:22:18: 9000000 INFO @ Fri, 10 Dec 2021 19:22:23: 16000000 INFO @ Fri, 10 Dec 2021 19:22:25: 7000000 INFO @ Fri, 10 Dec 2021 19:22:27: 10000000 INFO @ Fri, 10 Dec 2021 19:22:30: 17000000 INFO @ Fri, 10 Dec 2021 19:22:32: 8000000 INFO @ Fri, 10 Dec 2021 19:22:35: 11000000 INFO @ Fri, 10 Dec 2021 19:22:38: 18000000 INFO @ Fri, 10 Dec 2021 19:22:40: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:22:41: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:22:41: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:22:41: #1 total tags in treatment: 3360839 INFO @ Fri, 10 Dec 2021 19:22:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:22:41: #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 19:22:41: #1 tags after filtering in treatment: 2840415 INFO @ Fri, 10 Dec 2021 19:22:41: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:22:41: #1 finished! INFO @ Fri, 10 Dec 2021 19:22:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:22:42: #2 number of paired peaks: 3715 INFO @ Fri, 10 Dec 2021 19:22:42: start model_add_line... INFO @ Fri, 10 Dec 2021 19:22:42: start X-correlation... INFO @ Fri, 10 Dec 2021 19:22:42: end of X-cor INFO @ Fri, 10 Dec 2021 19:22:42: #2 finished! INFO @ Fri, 10 Dec 2021 19:22:42: #2 predicted fragment length is 147 bps INFO @ Fri, 10 Dec 2021 19:22:42: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 10 Dec 2021 19:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.05_model.r WARNING @ Fri, 10 Dec 2021 19:22:42: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:22:42: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Fri, 10 Dec 2021 19:22:42: #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 19:22:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:22:44: 12000000 INFO @ Fri, 10 Dec 2021 19:22:47: 10000000 INFO @ Fri, 10 Dec 2021 19:22:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.05_summits.bed INFO @ Fri, 10 Dec 2021 19:22:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8033 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:22:52: 13000000 INFO @ Fri, 10 Dec 2021 19:22:54: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:23:01: 14000000 INFO @ Fri, 10 Dec 2021 19:23:02: 12000000 INFO @ Fri, 10 Dec 2021 19:23:09: 15000000 INFO @ Fri, 10 Dec 2021 19:23:10: 13000000 INFO @ Fri, 10 Dec 2021 19:23:17: 14000000 INFO @ Fri, 10 Dec 2021 19:23:17: 16000000 INFO @ Fri, 10 Dec 2021 19:23:25: 15000000 INFO @ Fri, 10 Dec 2021 19:23:26: 17000000 INFO @ Fri, 10 Dec 2021 19:23:32: 16000000 INFO @ Fri, 10 Dec 2021 19:23:33: 18000000 INFO @ Fri, 10 Dec 2021 19:23:37: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:23:37: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:23:37: #1 total tags in treatment: 3360839 INFO @ Fri, 10 Dec 2021 19:23:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:37: #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 19:23:37: #1 tags after filtering in treatment: 2840415 INFO @ Fri, 10 Dec 2021 19:23:37: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:23:37: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:37: #2 number of paired peaks: 3715 INFO @ Fri, 10 Dec 2021 19:23:37: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:37: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:37: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:37: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:37: #2 predicted fragment length is 147 bps INFO @ Fri, 10 Dec 2021 19:23:37: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 10 Dec 2021 19:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.10_model.r WARNING @ Fri, 10 Dec 2021 19:23:37: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:37: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Fri, 10 Dec 2021 19:23:37: #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 19:23:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:39: 17000000 INFO @ Fri, 10 Dec 2021 19:23:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:45: 18000000 INFO @ Fri, 10 Dec 2021 19:23:48: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:23:48: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:23:48: #1 total tags in treatment: 3360839 INFO @ Fri, 10 Dec 2021 19:23:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:48: #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 19:23:48: #1 tags after filtering in treatment: 2840415 INFO @ Fri, 10 Dec 2021 19:23:48: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:23:48: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:48: #2 number of paired peaks: 3715 INFO @ Fri, 10 Dec 2021 19:23:48: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:48: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:48: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:48: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:48: #2 predicted fragment length is 147 bps INFO @ Fri, 10 Dec 2021 19:23:48: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 10 Dec 2021 19:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.20_model.r WARNING @ Fri, 10 Dec 2021 19:23:48: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:48: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Fri, 10 Dec 2021 19:23:48: #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 19:23:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.10_summits.bed INFO @ Fri, 10 Dec 2021 19:23:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3891 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:23:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978848/ERX3978848.20_summits.bed INFO @ Fri, 10 Dec 2021 19:23:58: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1054 records, 4 fields): 3 millis CompletedMACS2peakCalling