Job ID = 14172043 SRX = SRX9103807 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24235103 spots for SRR12621007/SRR12621007.sra Written 24235103 spots for SRR12621007/SRR12621007.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172545 ("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: 00:21:18 24235103 reads; of these: 24235103 (100.00%) were paired; of these: 8609112 (35.52%) aligned concordantly 0 times 8789080 (36.27%) aligned concordantly exactly 1 time 6836911 (28.21%) aligned concordantly >1 times ---- 8609112 pairs aligned concordantly 0 times; of these: 1478189 (17.17%) aligned discordantly 1 time ---- 7130923 pairs aligned 0 times concordantly or discordantly; of these: 14261846 mates make up the pairs; of these: 12468888 (87.43%) aligned 0 times 556457 (3.90%) aligned exactly 1 time 1236501 (8.67%) aligned >1 times 74.28% overall alignment rate Time searching: 00:21:18 Overall time: 00:21:18 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 16 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] 5056115 / 16914356 = 0.2989 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 @ Sat, 11 Dec 2021 14:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.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 @ Sat, 11 Dec 2021 14:23:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:23:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:23:16: 1000000 INFO @ Sat, 11 Dec 2021 14:23:20: 2000000 INFO @ Sat, 11 Dec 2021 14:23:24: 3000000 INFO @ Sat, 11 Dec 2021 14:23:29: 4000000 INFO @ Sat, 11 Dec 2021 14:23:33: 5000000 INFO @ Sat, 11 Dec 2021 14:23:37: 6000000 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 @ Sat, 11 Dec 2021 14:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.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 @ Sat, 11 Dec 2021 14:23:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:23:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:23:42: 7000000 INFO @ Sat, 11 Dec 2021 14:23:45: 1000000 INFO @ Sat, 11 Dec 2021 14:23:46: 8000000 INFO @ Sat, 11 Dec 2021 14:23:50: 2000000 INFO @ Sat, 11 Dec 2021 14:23:51: 9000000 INFO @ Sat, 11 Dec 2021 14:23:54: 3000000 INFO @ Sat, 11 Dec 2021 14:23:55: 10000000 INFO @ Sat, 11 Dec 2021 14:23:59: 4000000 INFO @ Sat, 11 Dec 2021 14:23:59: 11000000 INFO @ Sat, 11 Dec 2021 14:24:03: 5000000 INFO @ Sat, 11 Dec 2021 14:24:04: 12000000 INFO @ Sat, 11 Dec 2021 14:24:07: 6000000 INFO @ Sat, 11 Dec 2021 14:24:08: 13000000 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 @ Sat, 11 Dec 2021 14:24:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.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 @ Sat, 11 Dec 2021 14:24:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:24:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:24:12: 7000000 INFO @ Sat, 11 Dec 2021 14:24:13: 14000000 INFO @ Sat, 11 Dec 2021 14:24:16: 1000000 INFO @ Sat, 11 Dec 2021 14:24:16: 8000000 INFO @ Sat, 11 Dec 2021 14:24:17: 15000000 INFO @ Sat, 11 Dec 2021 14:24:21: 9000000 INFO @ Sat, 11 Dec 2021 14:24:21: 2000000 INFO @ Sat, 11 Dec 2021 14:24:22: 16000000 INFO @ Sat, 11 Dec 2021 14:24:26: 10000000 INFO @ Sat, 11 Dec 2021 14:24:26: 17000000 INFO @ Sat, 11 Dec 2021 14:24:27: 3000000 INFO @ Sat, 11 Dec 2021 14:24:30: 11000000 INFO @ Sat, 11 Dec 2021 14:24:31: 18000000 INFO @ Sat, 11 Dec 2021 14:24:32: 4000000 INFO @ Sat, 11 Dec 2021 14:24:35: 12000000 INFO @ Sat, 11 Dec 2021 14:24:35: 19000000 INFO @ Sat, 11 Dec 2021 14:24:37: 5000000 INFO @ Sat, 11 Dec 2021 14:24:39: 13000000 INFO @ Sat, 11 Dec 2021 14:24:39: 20000000 INFO @ Sat, 11 Dec 2021 14:24:43: 6000000 INFO @ Sat, 11 Dec 2021 14:24:44: 14000000 INFO @ Sat, 11 Dec 2021 14:24:44: 21000000 INFO @ Sat, 11 Dec 2021 14:24:48: 7000000 INFO @ Sat, 11 Dec 2021 14:24:48: 15000000 INFO @ Sat, 11 Dec 2021 14:24:48: 22000000 INFO @ Sat, 11 Dec 2021 14:24:53: 16000000 INFO @ Sat, 11 Dec 2021 14:24:53: 23000000 INFO @ Sat, 11 Dec 2021 14:24:53: 8000000 INFO @ Sat, 11 Dec 2021 14:24:57: 17000000 INFO @ Sat, 11 Dec 2021 14:24:57: 24000000 INFO @ Sat, 11 Dec 2021 14:24:58: 9000000 INFO @ Sat, 11 Dec 2021 14:25:01: 18000000 INFO @ Sat, 11 Dec 2021 14:25:02: 25000000 INFO @ Sat, 11 Dec 2021 14:25:04: 10000000 INFO @ Sat, 11 Dec 2021 14:25:06: 19000000 INFO @ Sat, 11 Dec 2021 14:25:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:06: #1 total tags in treatment: 10702505 INFO @ Sat, 11 Dec 2021 14:25:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:25:06: #1 tags after filtering in treatment: 8413375 INFO @ Sat, 11 Dec 2021 14:25:06: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:25:06: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:07: #2 number of paired peaks: 798 WARNING @ Sat, 11 Dec 2021 14:25:07: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Sat, 11 Dec 2021 14:25:07: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:07: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:07: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:07: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:07: #2 predicted fragment length is 77 bps INFO @ Sat, 11 Dec 2021 14:25:07: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 11 Dec 2021 14:25:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.05_model.r WARNING @ Sat, 11 Dec 2021 14:25:07: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:07: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 11 Dec 2021 14:25:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:25:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:25:09: 11000000 INFO @ Sat, 11 Dec 2021 14:25:10: 20000000 INFO @ Sat, 11 Dec 2021 14:25:14: 12000000 INFO @ Sat, 11 Dec 2021 14:25:15: 21000000 INFO @ Sat, 11 Dec 2021 14:25:19: 22000000 INFO @ Sat, 11 Dec 2021 14:25:19: 13000000 INFO @ Sat, 11 Dec 2021 14:25:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:25:24: 23000000 INFO @ Sat, 11 Dec 2021 14:25:24: 14000000 INFO @ Sat, 11 Dec 2021 14:25:28: 24000000 INFO @ Sat, 11 Dec 2021 14:25:30: 15000000 INFO @ Sat, 11 Dec 2021 14:25:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:25:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:25:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.05_summits.bed INFO @ Sat, 11 Dec 2021 14:25:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7923 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:25:33: 25000000 INFO @ Sat, 11 Dec 2021 14:25:35: 16000000 INFO @ Sat, 11 Dec 2021 14:25:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:25:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:25:37: #1 total tags in treatment: 10702505 INFO @ Sat, 11 Dec 2021 14:25:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:25:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:25:37: #1 tags after filtering in treatment: 8413375 INFO @ Sat, 11 Dec 2021 14:25:37: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:25:37: #1 finished! INFO @ Sat, 11 Dec 2021 14:25:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:25:37: #2 number of paired peaks: 798 WARNING @ Sat, 11 Dec 2021 14:25:37: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Sat, 11 Dec 2021 14:25:37: start model_add_line... INFO @ Sat, 11 Dec 2021 14:25:38: start X-correlation... INFO @ Sat, 11 Dec 2021 14:25:38: end of X-cor INFO @ Sat, 11 Dec 2021 14:25:38: #2 finished! INFO @ Sat, 11 Dec 2021 14:25:38: #2 predicted fragment length is 77 bps INFO @ Sat, 11 Dec 2021 14:25:38: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 11 Dec 2021 14:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.10_model.r WARNING @ Sat, 11 Dec 2021 14:25:38: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:25:38: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 11 Dec 2021 14:25:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:25:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:25:40: 17000000 INFO @ Sat, 11 Dec 2021 14:25:45: 18000000 INFO @ Sat, 11 Dec 2021 14:25:50: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:25:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:25:55: 20000000 INFO @ Sat, 11 Dec 2021 14:26:00: 21000000 INFO @ Sat, 11 Dec 2021 14:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.10_summits.bed INFO @ Sat, 11 Dec 2021 14:26:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3609 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:26:05: 22000000 INFO @ Sat, 11 Dec 2021 14:26:10: 23000000 INFO @ Sat, 11 Dec 2021 14:26:15: 24000000 INFO @ Sat, 11 Dec 2021 14:26:20: 25000000 INFO @ Sat, 11 Dec 2021 14:26:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:26:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:26:24: #1 total tags in treatment: 10702505 INFO @ Sat, 11 Dec 2021 14:26:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:26:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:26:25: #1 tags after filtering in treatment: 8413375 INFO @ Sat, 11 Dec 2021 14:26:25: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:26:25: #1 finished! INFO @ Sat, 11 Dec 2021 14:26:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:26:25: #2 number of paired peaks: 798 WARNING @ Sat, 11 Dec 2021 14:26:25: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Sat, 11 Dec 2021 14:26:25: start model_add_line... INFO @ Sat, 11 Dec 2021 14:26:25: start X-correlation... INFO @ Sat, 11 Dec 2021 14:26:25: end of X-cor INFO @ Sat, 11 Dec 2021 14:26:25: #2 finished! INFO @ Sat, 11 Dec 2021 14:26:25: #2 predicted fragment length is 77 bps INFO @ Sat, 11 Dec 2021 14:26:25: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 11 Dec 2021 14:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.20_model.r WARNING @ Sat, 11 Dec 2021 14:26:25: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:26:25: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 11 Dec 2021 14:26:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:26:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:26:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:26:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103807/SRX9103807.20_summits.bed INFO @ Sat, 11 Dec 2021 14:26:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 1 millis CompletedMACS2peakCalling