Job ID = 12265353 SRX = SRX6430369 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32387937 spots for SRR9669872/SRR9669872.sra Written 32387937 spots for SRR9669872/SRR9669872.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265540 ("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: 00:19:09 32387937 reads; of these: 32387937 (100.00%) were paired; of these: 20089785 (62.03%) aligned concordantly 0 times 7565126 (23.36%) aligned concordantly exactly 1 time 4733026 (14.61%) aligned concordantly >1 times ---- 20089785 pairs aligned concordantly 0 times; of these: 1409959 (7.02%) aligned discordantly 1 time ---- 18679826 pairs aligned 0 times concordantly or discordantly; of these: 37359652 mates make up the pairs; of these: 35906241 (96.11%) aligned 0 times 478908 (1.28%) aligned exactly 1 time 974503 (2.61%) aligned >1 times 44.57% overall alignment rate Time searching: 00:19:09 Overall time: 00:19:09 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 12 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] 2624325 / 13519038 = 0.1941 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 07:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.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 07:09:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:09:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:09:08: 1000000 INFO @ Sat, 03 Apr 2021 07:09:14: 2000000 INFO @ Sat, 03 Apr 2021 07:09:20: 3000000 INFO @ Sat, 03 Apr 2021 07:09:26: 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 07:09:32: 5000000 INFO @ Sat, 03 Apr 2021 07:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.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 07:09:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:09:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:09:38: 6000000 INFO @ Sat, 03 Apr 2021 07:09:38: 1000000 INFO @ Sat, 03 Apr 2021 07:09:44: 2000000 INFO @ Sat, 03 Apr 2021 07:09:44: 7000000 INFO @ Sat, 03 Apr 2021 07:09:50: 3000000 INFO @ Sat, 03 Apr 2021 07:09:50: 8000000 INFO @ Sat, 03 Apr 2021 07:09:56: 4000000 INFO @ Sat, 03 Apr 2021 07:09:56: 9000000 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 07:10:02: 5000000 INFO @ Sat, 03 Apr 2021 07:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.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 07:10:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:10:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:10:03: 10000000 INFO @ Sat, 03 Apr 2021 07:10:08: 6000000 INFO @ Sat, 03 Apr 2021 07:10:09: 1000000 INFO @ Sat, 03 Apr 2021 07:10:09: 11000000 INFO @ Sat, 03 Apr 2021 07:10:15: 7000000 INFO @ Sat, 03 Apr 2021 07:10:15: 12000000 INFO @ Sat, 03 Apr 2021 07:10:16: 2000000 INFO @ Sat, 03 Apr 2021 07:10:21: 8000000 INFO @ Sat, 03 Apr 2021 07:10:22: 13000000 INFO @ Sat, 03 Apr 2021 07:10:23: 3000000 INFO @ Sat, 03 Apr 2021 07:10:27: 9000000 INFO @ Sat, 03 Apr 2021 07:10:28: 14000000 INFO @ Sat, 03 Apr 2021 07:10:30: 4000000 INFO @ Sat, 03 Apr 2021 07:10:34: 10000000 INFO @ Sat, 03 Apr 2021 07:10:34: 15000000 INFO @ Sat, 03 Apr 2021 07:10:36: 5000000 INFO @ Sat, 03 Apr 2021 07:10:40: 11000000 INFO @ Sat, 03 Apr 2021 07:10:41: 16000000 INFO @ Sat, 03 Apr 2021 07:10:43: 6000000 INFO @ Sat, 03 Apr 2021 07:10:46: 12000000 INFO @ Sat, 03 Apr 2021 07:10:47: 17000000 INFO @ Sat, 03 Apr 2021 07:10:50: 7000000 INFO @ Sat, 03 Apr 2021 07:10:52: 13000000 INFO @ Sat, 03 Apr 2021 07:10:52: 18000000 INFO @ Sat, 03 Apr 2021 07:10:57: 8000000 INFO @ Sat, 03 Apr 2021 07:10:58: 19000000 INFO @ Sat, 03 Apr 2021 07:10:59: 14000000 INFO @ Sat, 03 Apr 2021 07:11:04: 9000000 INFO @ Sat, 03 Apr 2021 07:11:04: 20000000 INFO @ Sat, 03 Apr 2021 07:11:05: 15000000 INFO @ Sat, 03 Apr 2021 07:11:10: 10000000 INFO @ Sat, 03 Apr 2021 07:11:11: 21000000 INFO @ Sat, 03 Apr 2021 07:11:11: 16000000 INFO @ Sat, 03 Apr 2021 07:11:17: 22000000 INFO @ Sat, 03 Apr 2021 07:11:17: 11000000 INFO @ Sat, 03 Apr 2021 07:11:17: 17000000 INFO @ Sat, 03 Apr 2021 07:11:23: 23000000 INFO @ Sat, 03 Apr 2021 07:11:23: 18000000 INFO @ Sat, 03 Apr 2021 07:11:24: 12000000 INFO @ Sat, 03 Apr 2021 07:11:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:11:26: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:11:26: #1 total tags in treatment: 9747268 INFO @ Sat, 03 Apr 2021 07:11:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:11:26: #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 07:11:27: #1 tags after filtering in treatment: 8071491 INFO @ Sat, 03 Apr 2021 07:11:27: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 07:11:27: #1 finished! INFO @ Sat, 03 Apr 2021 07:11:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:11:27: #2 number of paired peaks: 113 WARNING @ Sat, 03 Apr 2021 07:11:27: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 03 Apr 2021 07:11:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:11:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:11:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:11:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:11:27: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 07:11:27: #2 alternative fragment length(s) may be 3,50,460,534 bps INFO @ Sat, 03 Apr 2021 07:11:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.05_model.r WARNING @ Sat, 03 Apr 2021 07:11:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:11:27: #2 You may need to consider one of the other alternative d(s): 3,50,460,534 WARNING @ Sat, 03 Apr 2021 07:11:27: #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 07:11:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:11:29: 19000000 INFO @ Sat, 03 Apr 2021 07:11:31: 13000000 INFO @ Sat, 03 Apr 2021 07:11:35: 20000000 INFO @ Sat, 03 Apr 2021 07:11:37: 14000000 INFO @ Sat, 03 Apr 2021 07:11:41: 21000000 INFO @ Sat, 03 Apr 2021 07:11:44: 15000000 INFO @ Sat, 03 Apr 2021 07:11:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:11:47: 22000000 INFO @ Sat, 03 Apr 2021 07:11:50: 16000000 INFO @ Sat, 03 Apr 2021 07:11:53: 23000000 INFO @ Sat, 03 Apr 2021 07:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.05_summits.bed INFO @ Sat, 03 Apr 2021 07:11:56: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1421 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:11:57: 17000000 INFO @ Sat, 03 Apr 2021 07:11:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:11:57: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:11:57: #1 total tags in treatment: 9747268 INFO @ Sat, 03 Apr 2021 07:11:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:11:57: #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 07:11:57: #1 tags after filtering in treatment: 8071491 INFO @ Sat, 03 Apr 2021 07:11:57: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 07:11:57: #1 finished! INFO @ Sat, 03 Apr 2021 07:11:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:11:58: #2 number of paired peaks: 113 WARNING @ Sat, 03 Apr 2021 07:11:58: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 03 Apr 2021 07:11:58: start model_add_line... INFO @ Sat, 03 Apr 2021 07:11:58: start X-correlation... INFO @ Sat, 03 Apr 2021 07:11:58: end of X-cor INFO @ Sat, 03 Apr 2021 07:11:58: #2 finished! INFO @ Sat, 03 Apr 2021 07:11:58: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 07:11:58: #2 alternative fragment length(s) may be 3,50,460,534 bps INFO @ Sat, 03 Apr 2021 07:11:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.10_model.r WARNING @ Sat, 03 Apr 2021 07:11:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:11:58: #2 You may need to consider one of the other alternative d(s): 3,50,460,534 WARNING @ Sat, 03 Apr 2021 07:11:58: #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 07:11:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:12:03: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:12:09: 19000000 INFO @ Sat, 03 Apr 2021 07:12:15: 20000000 INFO @ Sat, 03 Apr 2021 07:12:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:12:21: 21000000 INFO @ Sat, 03 Apr 2021 07:12:27: 22000000 INFO @ Sat, 03 Apr 2021 07:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.10_summits.bed INFO @ Sat, 03 Apr 2021 07:12:27: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:12:33: 23000000 INFO @ Sat, 03 Apr 2021 07:12:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:12:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:12:37: #1 total tags in treatment: 9747268 INFO @ Sat, 03 Apr 2021 07:12:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:12:37: #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 07:12:37: #1 tags after filtering in treatment: 8071491 INFO @ Sat, 03 Apr 2021 07:12:37: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 07:12:37: #1 finished! INFO @ Sat, 03 Apr 2021 07:12:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:12:37: #2 number of paired peaks: 113 WARNING @ Sat, 03 Apr 2021 07:12:37: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 03 Apr 2021 07:12:37: start model_add_line... INFO @ Sat, 03 Apr 2021 07:12:37: start X-correlation... INFO @ Sat, 03 Apr 2021 07:12:37: end of X-cor INFO @ Sat, 03 Apr 2021 07:12:37: #2 finished! INFO @ Sat, 03 Apr 2021 07:12:37: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 07:12:37: #2 alternative fragment length(s) may be 3,50,460,534 bps INFO @ Sat, 03 Apr 2021 07:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.20_model.r WARNING @ Sat, 03 Apr 2021 07:12:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:12:37: #2 You may need to consider one of the other alternative d(s): 3,50,460,534 WARNING @ Sat, 03 Apr 2021 07:12:37: #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 07:12:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:12:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:12:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430369/SRX6430369.20_summits.bed INFO @ Sat, 03 Apr 2021 07:13:05: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis CompletedMACS2peakCalling