Job ID = 12265569 SRX = SRX7277028 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24479668 spots for SRR10597293/SRR10597293.sra Written 24479668 spots for SRR10597293/SRR10597293.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265809 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:31:46 24479668 reads; of these: 24479668 (100.00%) were paired; of these: 9575485 (39.12%) aligned concordantly 0 times 10401008 (42.49%) aligned concordantly exactly 1 time 4503175 (18.40%) aligned concordantly >1 times ---- 9575485 pairs aligned concordantly 0 times; of these: 2467333 (25.77%) aligned discordantly 1 time ---- 7108152 pairs aligned 0 times concordantly or discordantly; of these: 14216304 mates make up the pairs; of these: 11586007 (81.50%) aligned 0 times 698301 (4.91%) aligned exactly 1 time 1931996 (13.59%) aligned >1 times 76.34% overall alignment rate Time searching: 00:31:47 Overall time: 00:31:47 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] 2639199 / 17238082 = 0.1531 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.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, 03 Apr 2021 08:24:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:24:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:24:34: 1000000 INFO @ Sat, 03 Apr 2021 08:24:40: 2000000 INFO @ Sat, 03 Apr 2021 08:24:46: 3000000 INFO @ Sat, 03 Apr 2021 08:24:52: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.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, 03 Apr 2021 08:24:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:24:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:24:58: 5000000 INFO @ Sat, 03 Apr 2021 08:25:05: 1000000 INFO @ Sat, 03 Apr 2021 08:25:05: 6000000 INFO @ Sat, 03 Apr 2021 08:25:12: 7000000 INFO @ Sat, 03 Apr 2021 08:25:12: 2000000 INFO @ Sat, 03 Apr 2021 08:25:19: 8000000 INFO @ Sat, 03 Apr 2021 08:25:20: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:25:26: 9000000 INFO @ Sat, 03 Apr 2021 08:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.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, 03 Apr 2021 08:25:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:25:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:25:27: 4000000 INFO @ Sat, 03 Apr 2021 08:25:33: 10000000 INFO @ Sat, 03 Apr 2021 08:25:35: 1000000 INFO @ Sat, 03 Apr 2021 08:25:35: 5000000 INFO @ Sat, 03 Apr 2021 08:25:40: 11000000 INFO @ Sat, 03 Apr 2021 08:25:42: 2000000 INFO @ Sat, 03 Apr 2021 08:25:43: 6000000 INFO @ Sat, 03 Apr 2021 08:25:47: 12000000 INFO @ Sat, 03 Apr 2021 08:25:49: 3000000 INFO @ Sat, 03 Apr 2021 08:25:50: 7000000 INFO @ Sat, 03 Apr 2021 08:25:55: 13000000 INFO @ Sat, 03 Apr 2021 08:25:56: 4000000 INFO @ Sat, 03 Apr 2021 08:25:58: 8000000 INFO @ Sat, 03 Apr 2021 08:26:02: 14000000 INFO @ Sat, 03 Apr 2021 08:26:03: 5000000 INFO @ Sat, 03 Apr 2021 08:26:06: 9000000 INFO @ Sat, 03 Apr 2021 08:26:09: 15000000 INFO @ Sat, 03 Apr 2021 08:26:11: 6000000 INFO @ Sat, 03 Apr 2021 08:26:13: 10000000 INFO @ Sat, 03 Apr 2021 08:26:16: 16000000 INFO @ Sat, 03 Apr 2021 08:26:18: 7000000 INFO @ Sat, 03 Apr 2021 08:26:21: 11000000 INFO @ Sat, 03 Apr 2021 08:26:23: 17000000 INFO @ Sat, 03 Apr 2021 08:26:25: 8000000 INFO @ Sat, 03 Apr 2021 08:26:29: 12000000 INFO @ Sat, 03 Apr 2021 08:26:30: 18000000 INFO @ Sat, 03 Apr 2021 08:26:32: 9000000 INFO @ Sat, 03 Apr 2021 08:26:37: 13000000 INFO @ Sat, 03 Apr 2021 08:26:37: 19000000 INFO @ Sat, 03 Apr 2021 08:26:39: 10000000 INFO @ Sat, 03 Apr 2021 08:26:44: 14000000 INFO @ Sat, 03 Apr 2021 08:26:45: 20000000 INFO @ Sat, 03 Apr 2021 08:26:46: 11000000 INFO @ Sat, 03 Apr 2021 08:26:52: 21000000 INFO @ Sat, 03 Apr 2021 08:26:52: 15000000 INFO @ Sat, 03 Apr 2021 08:26:53: 12000000 INFO @ Sat, 03 Apr 2021 08:26:59: 22000000 INFO @ Sat, 03 Apr 2021 08:27:00: 16000000 INFO @ Sat, 03 Apr 2021 08:27:01: 13000000 INFO @ Sat, 03 Apr 2021 08:27:05: 23000000 INFO @ Sat, 03 Apr 2021 08:27:07: 17000000 INFO @ Sat, 03 Apr 2021 08:27:08: 14000000 INFO @ Sat, 03 Apr 2021 08:27:12: 24000000 INFO @ Sat, 03 Apr 2021 08:27:15: 15000000 INFO @ Sat, 03 Apr 2021 08:27:15: 18000000 INFO @ Sat, 03 Apr 2021 08:27:19: 25000000 INFO @ Sat, 03 Apr 2021 08:27:21: 16000000 INFO @ Sat, 03 Apr 2021 08:27:23: 19000000 INFO @ Sat, 03 Apr 2021 08:27:26: 26000000 INFO @ Sat, 03 Apr 2021 08:27:29: 17000000 INFO @ Sat, 03 Apr 2021 08:27:30: 20000000 INFO @ Sat, 03 Apr 2021 08:27:33: 27000000 INFO @ Sat, 03 Apr 2021 08:27:36: 18000000 INFO @ Sat, 03 Apr 2021 08:27:38: 21000000 INFO @ Sat, 03 Apr 2021 08:27:40: 28000000 INFO @ Sat, 03 Apr 2021 08:27:43: 19000000 INFO @ Sat, 03 Apr 2021 08:27:46: 22000000 INFO @ Sat, 03 Apr 2021 08:27:48: 29000000 INFO @ Sat, 03 Apr 2021 08:27:50: 20000000 INFO @ Sat, 03 Apr 2021 08:27:53: 23000000 INFO @ Sat, 03 Apr 2021 08:27:55: 30000000 INFO @ Sat, 03 Apr 2021 08:27:57: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:28:01: 24000000 INFO @ Sat, 03 Apr 2021 08:28:02: 31000000 INFO @ Sat, 03 Apr 2021 08:28:04: 22000000 INFO @ Sat, 03 Apr 2021 08:28:08: 25000000 INFO @ Sat, 03 Apr 2021 08:28:09: 32000000 INFO @ Sat, 03 Apr 2021 08:28:10: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:28:10: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:28:10: #1 total tags in treatment: 12379774 INFO @ Sat, 03 Apr 2021 08:28:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:28:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:28:10: #1 tags after filtering in treatment: 9803195 INFO @ Sat, 03 Apr 2021 08:28:10: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:28:10: #1 finished! INFO @ Sat, 03 Apr 2021 08:28:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:28:11: #2 number of paired peaks: 401 WARNING @ Sat, 03 Apr 2021 08:28:11: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sat, 03 Apr 2021 08:28:11: start model_add_line... INFO @ Sat, 03 Apr 2021 08:28:11: start X-correlation... INFO @ Sat, 03 Apr 2021 08:28:11: end of X-cor INFO @ Sat, 03 Apr 2021 08:28:11: #2 finished! INFO @ Sat, 03 Apr 2021 08:28:11: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 08:28:11: #2 alternative fragment length(s) may be 4,78 bps INFO @ Sat, 03 Apr 2021 08:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.05_model.r WARNING @ Sat, 03 Apr 2021 08:28:11: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:28:11: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Sat, 03 Apr 2021 08:28:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:28:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:28:11: 23000000 INFO @ Sat, 03 Apr 2021 08:28:16: 26000000 INFO @ Sat, 03 Apr 2021 08:28:18: 24000000 INFO @ Sat, 03 Apr 2021 08:28:24: 27000000 INFO @ Sat, 03 Apr 2021 08:28:25: 25000000 INFO @ Sat, 03 Apr 2021 08:28:31: 28000000 INFO @ Sat, 03 Apr 2021 08:28:32: 26000000 INFO @ Sat, 03 Apr 2021 08:28:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:28:39: 27000000 INFO @ Sat, 03 Apr 2021 08:28:39: 29000000 INFO @ Sat, 03 Apr 2021 08:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.05_summits.bed INFO @ Sat, 03 Apr 2021 08:28:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7531 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:28:46: 28000000 INFO @ Sat, 03 Apr 2021 08:28:47: 30000000 INFO @ Sat, 03 Apr 2021 08:28:53: 29000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:28:54: 31000000 INFO @ Sat, 03 Apr 2021 08:29:00: 30000000 INFO @ Sat, 03 Apr 2021 08:29:02: 32000000 INFO @ Sat, 03 Apr 2021 08:29:03: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:29:03: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:29:03: #1 total tags in treatment: 12379774 INFO @ Sat, 03 Apr 2021 08:29:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:29:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:29:03: #1 tags after filtering in treatment: 9803195 INFO @ Sat, 03 Apr 2021 08:29:03: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:29:03: #1 finished! INFO @ Sat, 03 Apr 2021 08:29:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:29:04: #2 number of paired peaks: 401 WARNING @ Sat, 03 Apr 2021 08:29:04: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sat, 03 Apr 2021 08:29:04: start model_add_line... INFO @ Sat, 03 Apr 2021 08:29:04: start X-correlation... INFO @ Sat, 03 Apr 2021 08:29:04: end of X-cor INFO @ Sat, 03 Apr 2021 08:29:04: #2 finished! INFO @ Sat, 03 Apr 2021 08:29:04: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 08:29:04: #2 alternative fragment length(s) may be 4,78 bps INFO @ Sat, 03 Apr 2021 08:29:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.10_model.r WARNING @ Sat, 03 Apr 2021 08:29:04: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:29:04: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Sat, 03 Apr 2021 08:29:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:29:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:29:07: 31000000 INFO @ Sat, 03 Apr 2021 08:29:13: 32000000 INFO @ Sat, 03 Apr 2021 08:29:14: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:29:14: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:29:14: #1 total tags in treatment: 12379774 INFO @ Sat, 03 Apr 2021 08:29:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:29:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:29:14: #1 tags after filtering in treatment: 9803195 INFO @ Sat, 03 Apr 2021 08:29:14: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:29:14: #1 finished! INFO @ Sat, 03 Apr 2021 08:29:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:29:15: #2 number of paired peaks: 401 WARNING @ Sat, 03 Apr 2021 08:29:15: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sat, 03 Apr 2021 08:29:15: start model_add_line... INFO @ Sat, 03 Apr 2021 08:29:15: start X-correlation... INFO @ Sat, 03 Apr 2021 08:29:15: end of X-cor INFO @ Sat, 03 Apr 2021 08:29:15: #2 finished! INFO @ Sat, 03 Apr 2021 08:29:15: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 08:29:15: #2 alternative fragment length(s) may be 4,78 bps INFO @ Sat, 03 Apr 2021 08:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.20_model.r WARNING @ Sat, 03 Apr 2021 08:29:15: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:29:15: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Sat, 03 Apr 2021 08:29:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:29:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:29:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:29:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.10_summits.bed INFO @ Sat, 03 Apr 2021 08:29:39: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1774 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277028/SRX7277028.20_summits.bed INFO @ Sat, 03 Apr 2021 08:29:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling