Job ID = 14167969 SRX = ERX3978923 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29759300 spots for ERR3975992/ERR3975992.sra Written 29759300 spots for ERR3975992/ERR3975992.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168862 ("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: 01:23:33 29759300 reads; of these: 29759300 (100.00%) were paired; of these: 4109911 (13.81%) aligned concordantly 0 times 19566762 (65.75%) aligned concordantly exactly 1 time 6082627 (20.44%) aligned concordantly >1 times ---- 4109911 pairs aligned concordantly 0 times; of these: 810691 (19.73%) aligned discordantly 1 time ---- 3299220 pairs aligned 0 times concordantly or discordantly; of these: 6598440 mates make up the pairs; of these: 3111001 (47.15%) aligned 0 times 1727901 (26.19%) aligned exactly 1 time 1759538 (26.67%) aligned >1 times 94.77% overall alignment rate Time searching: 01:23:34 Overall time: 01:23:34 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 24 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] 14903690 / 26250737 = 0.5677 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 15:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.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 15:36:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:36:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:36:21: 1000000 INFO @ Fri, 10 Dec 2021 15:36:26: 2000000 INFO @ Fri, 10 Dec 2021 15:36:32: 3000000 INFO @ Fri, 10 Dec 2021 15:36:38: 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 15:36:43: 5000000 INFO @ Fri, 10 Dec 2021 15:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.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 15:36:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:36:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:36:50: 6000000 INFO @ Fri, 10 Dec 2021 15:36:51: 1000000 INFO @ Fri, 10 Dec 2021 15:36:56: 7000000 INFO @ Fri, 10 Dec 2021 15:36:58: 2000000 INFO @ Fri, 10 Dec 2021 15:37:03: 8000000 INFO @ Fri, 10 Dec 2021 15:37:05: 3000000 INFO @ Fri, 10 Dec 2021 15:37:10: 9000000 INFO @ Fri, 10 Dec 2021 15:37:12: 4000000 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 15:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.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 15:37:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:37:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:37:17: 10000000 INFO @ Fri, 10 Dec 2021 15:37:19: 5000000 INFO @ Fri, 10 Dec 2021 15:37:23: 1000000 INFO @ Fri, 10 Dec 2021 15:37:24: 11000000 INFO @ Fri, 10 Dec 2021 15:37:26: 6000000 INFO @ Fri, 10 Dec 2021 15:37:31: 2000000 INFO @ Fri, 10 Dec 2021 15:37:31: 12000000 INFO @ Fri, 10 Dec 2021 15:37:34: 7000000 INFO @ Fri, 10 Dec 2021 15:37:39: 13000000 INFO @ Fri, 10 Dec 2021 15:37:39: 3000000 INFO @ Fri, 10 Dec 2021 15:37:42: 8000000 INFO @ Fri, 10 Dec 2021 15:37:46: 14000000 INFO @ Fri, 10 Dec 2021 15:37:47: 4000000 INFO @ Fri, 10 Dec 2021 15:37:49: 9000000 INFO @ Fri, 10 Dec 2021 15:37:54: 15000000 INFO @ Fri, 10 Dec 2021 15:37:55: 5000000 INFO @ Fri, 10 Dec 2021 15:37:57: 10000000 INFO @ Fri, 10 Dec 2021 15:38:01: 16000000 INFO @ Fri, 10 Dec 2021 15:38:04: 6000000 INFO @ Fri, 10 Dec 2021 15:38:04: 11000000 INFO @ Fri, 10 Dec 2021 15:38:08: 17000000 INFO @ Fri, 10 Dec 2021 15:38:12: 7000000 INFO @ Fri, 10 Dec 2021 15:38:12: 12000000 INFO @ Fri, 10 Dec 2021 15:38:16: 18000000 INFO @ Fri, 10 Dec 2021 15:38:19: 13000000 INFO @ Fri, 10 Dec 2021 15:38:20: 8000000 INFO @ Fri, 10 Dec 2021 15:38:23: 19000000 INFO @ Fri, 10 Dec 2021 15:38:27: 14000000 INFO @ Fri, 10 Dec 2021 15:38:28: 9000000 INFO @ Fri, 10 Dec 2021 15:38:31: 20000000 INFO @ Fri, 10 Dec 2021 15:38:34: 15000000 INFO @ Fri, 10 Dec 2021 15:38:36: 10000000 INFO @ Fri, 10 Dec 2021 15:38:39: 21000000 INFO @ Fri, 10 Dec 2021 15:38:42: 16000000 INFO @ Fri, 10 Dec 2021 15:38:44: 11000000 INFO @ Fri, 10 Dec 2021 15:38:46: 22000000 INFO @ Fri, 10 Dec 2021 15:38:49: 17000000 INFO @ Fri, 10 Dec 2021 15:38:53: 12000000 INFO @ Fri, 10 Dec 2021 15:38:54: 23000000 INFO @ Fri, 10 Dec 2021 15:38:57: 18000000 INFO @ Fri, 10 Dec 2021 15:39:01: 13000000 INFO @ Fri, 10 Dec 2021 15:39:01: 24000000 INFO @ Fri, 10 Dec 2021 15:39:04: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:39:09: 25000000 INFO @ Fri, 10 Dec 2021 15:39:09: 14000000 INFO @ Fri, 10 Dec 2021 15:39:12: 20000000 INFO @ Fri, 10 Dec 2021 15:39:16: 26000000 INFO @ Fri, 10 Dec 2021 15:39:17: 15000000 INFO @ Fri, 10 Dec 2021 15:39:19: 21000000 INFO @ Fri, 10 Dec 2021 15:39:20: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 15:39:20: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 15:39:20: #1 total tags in treatment: 11167835 INFO @ Fri, 10 Dec 2021 15:39:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:39:20: #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 15:39:21: #1 tags after filtering in treatment: 10424975 INFO @ Fri, 10 Dec 2021 15:39:21: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 15:39:21: #1 finished! INFO @ Fri, 10 Dec 2021 15:39:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:39:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:39:21: #2 number of paired peaks: 381 WARNING @ Fri, 10 Dec 2021 15:39:21: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 10 Dec 2021 15:39:21: start model_add_line... INFO @ Fri, 10 Dec 2021 15:39:21: start X-correlation... INFO @ Fri, 10 Dec 2021 15:39:21: end of X-cor INFO @ Fri, 10 Dec 2021 15:39:21: #2 finished! INFO @ Fri, 10 Dec 2021 15:39:21: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Dec 2021 15:39:21: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Dec 2021 15:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.05_model.r WARNING @ Fri, 10 Dec 2021 15:39:21: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:39:21: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 10 Dec 2021 15:39:21: #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 15:39:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:39:25: 16000000 INFO @ Fri, 10 Dec 2021 15:39:27: 22000000 INFO @ Fri, 10 Dec 2021 15:39:33: 17000000 INFO @ Fri, 10 Dec 2021 15:39:34: 23000000 INFO @ Fri, 10 Dec 2021 15:39:41: 18000000 INFO @ Fri, 10 Dec 2021 15:39:41: 24000000 INFO @ Fri, 10 Dec 2021 15:39:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:39:49: 25000000 INFO @ Fri, 10 Dec 2021 15:39:49: 19000000 INFO @ Fri, 10 Dec 2021 15:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.05_summits.bed INFO @ Fri, 10 Dec 2021 15:39:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6687 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:39:56: 26000000 INFO @ Fri, 10 Dec 2021 15:39:57: 20000000 INFO @ Fri, 10 Dec 2021 15:40:00: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 15:40:00: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 15:40:00: #1 total tags in treatment: 11167835 INFO @ Fri, 10 Dec 2021 15:40:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:40:00: #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 15:40:00: #1 tags after filtering in treatment: 10424975 INFO @ Fri, 10 Dec 2021 15:40:00: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 15:40:00: #1 finished! INFO @ Fri, 10 Dec 2021 15:40:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:40:00: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:40:01: #2 number of paired peaks: 381 WARNING @ Fri, 10 Dec 2021 15:40:01: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 10 Dec 2021 15:40:01: start model_add_line... INFO @ Fri, 10 Dec 2021 15:40:01: start X-correlation... INFO @ Fri, 10 Dec 2021 15:40:01: end of X-cor INFO @ Fri, 10 Dec 2021 15:40:01: #2 finished! INFO @ Fri, 10 Dec 2021 15:40:01: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Dec 2021 15:40:01: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Dec 2021 15:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.10_model.r WARNING @ Fri, 10 Dec 2021 15:40:01: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:40:01: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 10 Dec 2021 15:40:01: #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 15:40:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:40:05: 21000000 INFO @ Fri, 10 Dec 2021 15:40:13: 22000000 INFO @ Fri, 10 Dec 2021 15:40:20: 23000000 INFO @ Fri, 10 Dec 2021 15:40:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:40:27: 24000000 INFO @ Fri, 10 Dec 2021 15:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.10_summits.bed INFO @ Fri, 10 Dec 2021 15:40:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2550 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:40:34: 25000000 INFO @ Fri, 10 Dec 2021 15:40:41: 26000000 INFO @ Fri, 10 Dec 2021 15:40:45: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 15:40:45: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 15:40:45: #1 total tags in treatment: 11167835 INFO @ Fri, 10 Dec 2021 15:40:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:40:45: #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 15:40:46: #1 tags after filtering in treatment: 10424975 INFO @ Fri, 10 Dec 2021 15:40:46: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 15:40:46: #1 finished! INFO @ Fri, 10 Dec 2021 15:40:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:40:46: #2 number of paired peaks: 381 WARNING @ Fri, 10 Dec 2021 15:40:46: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 10 Dec 2021 15:40:46: start model_add_line... INFO @ Fri, 10 Dec 2021 15:40:46: start X-correlation... INFO @ Fri, 10 Dec 2021 15:40:47: end of X-cor INFO @ Fri, 10 Dec 2021 15:40:47: #2 finished! INFO @ Fri, 10 Dec 2021 15:40:47: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Dec 2021 15:40:47: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Dec 2021 15:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.20_model.r WARNING @ Fri, 10 Dec 2021 15:40:47: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:40:47: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 10 Dec 2021 15:40:47: #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 15:40:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:41:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:41:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978923/ERX3978923.20_summits.bed INFO @ Fri, 10 Dec 2021 15:41:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (941 records, 4 fields): 3 millis CompletedMACS2peakCalling