Job ID = 6626499 SRX = SRX5736478 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14450951 spots for SRR8956889/SRR8956889.sra Written 14450951 spots for SRR8956889/SRR8956889.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626720 ("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: 00:38:16 14450951 reads; of these: 14450951 (100.00%) were paired; of these: 2560917 (17.72%) aligned concordantly 0 times 7853200 (54.34%) aligned concordantly exactly 1 time 4036834 (27.93%) aligned concordantly >1 times ---- 2560917 pairs aligned concordantly 0 times; of these: 503312 (19.65%) aligned discordantly 1 time ---- 2057605 pairs aligned 0 times concordantly or discordantly; of these: 4115210 mates make up the pairs; of these: 2688259 (65.32%) aligned 0 times 613052 (14.90%) aligned exactly 1 time 813899 (19.78%) aligned >1 times 90.70% overall alignment rate Time searching: 00:38:16 Overall time: 00:38:16 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] 1386970 / 12312826 = 0.1126 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.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 @ Tue, 14 Jul 2020 07:55:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:55:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:55:24: 1000000 INFO @ Tue, 14 Jul 2020 07:55:31: 2000000 INFO @ Tue, 14 Jul 2020 07:55:37: 3000000 INFO @ Tue, 14 Jul 2020 07:55:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.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 @ Tue, 14 Jul 2020 07:55:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:55:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:55:50: 5000000 INFO @ Tue, 14 Jul 2020 07:55:55: 1000000 INFO @ Tue, 14 Jul 2020 07:55:57: 6000000 INFO @ Tue, 14 Jul 2020 07:56:02: 2000000 INFO @ Tue, 14 Jul 2020 07:56:03: 7000000 INFO @ Tue, 14 Jul 2020 07:56:09: 3000000 INFO @ Tue, 14 Jul 2020 07:56:11: 8000000 INFO @ Tue, 14 Jul 2020 07:56:16: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.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 @ Tue, 14 Jul 2020 07:56:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:56:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:56:18: 9000000 INFO @ Tue, 14 Jul 2020 07:56:23: 5000000 INFO @ Tue, 14 Jul 2020 07:56:25: 1000000 INFO @ Tue, 14 Jul 2020 07:56:25: 10000000 INFO @ Tue, 14 Jul 2020 07:56:29: 6000000 INFO @ Tue, 14 Jul 2020 07:56:31: 2000000 INFO @ Tue, 14 Jul 2020 07:56:33: 11000000 INFO @ Tue, 14 Jul 2020 07:56:36: 7000000 INFO @ Tue, 14 Jul 2020 07:56:39: 3000000 INFO @ Tue, 14 Jul 2020 07:56:40: 12000000 INFO @ Tue, 14 Jul 2020 07:56:43: 8000000 INFO @ Tue, 14 Jul 2020 07:56:45: 4000000 INFO @ Tue, 14 Jul 2020 07:56:47: 13000000 INFO @ Tue, 14 Jul 2020 07:56:50: 9000000 INFO @ Tue, 14 Jul 2020 07:56:51: 5000000 INFO @ Tue, 14 Jul 2020 07:56:55: 14000000 INFO @ Tue, 14 Jul 2020 07:56:57: 10000000 INFO @ Tue, 14 Jul 2020 07:56:59: 6000000 INFO @ Tue, 14 Jul 2020 07:57:02: 15000000 INFO @ Tue, 14 Jul 2020 07:57:04: 11000000 INFO @ Tue, 14 Jul 2020 07:57:05: 7000000 INFO @ Tue, 14 Jul 2020 07:57:09: 16000000 INFO @ Tue, 14 Jul 2020 07:57:11: 12000000 INFO @ Tue, 14 Jul 2020 07:57:12: 8000000 INFO @ Tue, 14 Jul 2020 07:57:17: 17000000 INFO @ Tue, 14 Jul 2020 07:57:18: 9000000 INFO @ Tue, 14 Jul 2020 07:57:18: 13000000 INFO @ Tue, 14 Jul 2020 07:57:24: 18000000 INFO @ Tue, 14 Jul 2020 07:57:24: 10000000 INFO @ Tue, 14 Jul 2020 07:57:25: 14000000 INFO @ Tue, 14 Jul 2020 07:57:31: 11000000 INFO @ Tue, 14 Jul 2020 07:57:31: 19000000 INFO @ Tue, 14 Jul 2020 07:57:33: 15000000 INFO @ Tue, 14 Jul 2020 07:57:37: 12000000 INFO @ Tue, 14 Jul 2020 07:57:39: 20000000 INFO @ Tue, 14 Jul 2020 07:57:40: 16000000 INFO @ Tue, 14 Jul 2020 07:57:43: 13000000 INFO @ Tue, 14 Jul 2020 07:57:46: 21000000 INFO @ Tue, 14 Jul 2020 07:57:47: 17000000 INFO @ Tue, 14 Jul 2020 07:57:50: 14000000 INFO @ Tue, 14 Jul 2020 07:57:53: 22000000 INFO @ Tue, 14 Jul 2020 07:57:54: 18000000 INFO @ Tue, 14 Jul 2020 07:57:56: 15000000 INFO @ Tue, 14 Jul 2020 07:58:01: 23000000 INFO @ Tue, 14 Jul 2020 07:58:02: 19000000 INFO @ Tue, 14 Jul 2020 07:58:02: 16000000 INFO @ Tue, 14 Jul 2020 07:58:04: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:58:04: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:58:04: #1 total tags in treatment: 10535154 INFO @ Tue, 14 Jul 2020 07:58:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:58:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:58:04: #1 tags after filtering in treatment: 9516013 INFO @ Tue, 14 Jul 2020 07:58:04: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:58:04: #1 finished! INFO @ Tue, 14 Jul 2020 07:58:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:58:05: #2 number of paired peaks: 122 WARNING @ Tue, 14 Jul 2020 07:58:05: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 14 Jul 2020 07:58:05: start model_add_line... INFO @ Tue, 14 Jul 2020 07:58:05: start X-correlation... INFO @ Tue, 14 Jul 2020 07:58:05: end of X-cor INFO @ Tue, 14 Jul 2020 07:58:05: #2 finished! INFO @ Tue, 14 Jul 2020 07:58:05: #2 predicted fragment length is 127 bps INFO @ Tue, 14 Jul 2020 07:58:05: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 14 Jul 2020 07:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.05_model.r WARNING @ Tue, 14 Jul 2020 07:58:05: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:58:05: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Tue, 14 Jul 2020 07:58:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:58:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:58:09: 17000000 INFO @ Tue, 14 Jul 2020 07:58:09: 20000000 INFO @ Tue, 14 Jul 2020 07:58:15: 18000000 INFO @ Tue, 14 Jul 2020 07:58:16: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:58:21: 19000000 INFO @ Tue, 14 Jul 2020 07:58:23: 22000000 INFO @ Tue, 14 Jul 2020 07:58:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:58:27: 20000000 INFO @ Tue, 14 Jul 2020 07:58:30: 23000000 INFO @ Tue, 14 Jul 2020 07:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.05_summits.bed INFO @ Tue, 14 Jul 2020 07:58:33: Done! INFO @ Tue, 14 Jul 2020 07:58:33: 21000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1416 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:58:34: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:58:34: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:58:34: #1 total tags in treatment: 10535154 INFO @ Tue, 14 Jul 2020 07:58:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:58:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:58:34: #1 tags after filtering in treatment: 9516013 INFO @ Tue, 14 Jul 2020 07:58:34: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:58:34: #1 finished! INFO @ Tue, 14 Jul 2020 07:58:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:58:34: #2 number of paired peaks: 122 WARNING @ Tue, 14 Jul 2020 07:58:34: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 14 Jul 2020 07:58:34: start model_add_line... INFO @ Tue, 14 Jul 2020 07:58:34: start X-correlation... INFO @ Tue, 14 Jul 2020 07:58:34: end of X-cor INFO @ Tue, 14 Jul 2020 07:58:34: #2 finished! INFO @ Tue, 14 Jul 2020 07:58:34: #2 predicted fragment length is 127 bps INFO @ Tue, 14 Jul 2020 07:58:34: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 14 Jul 2020 07:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.10_model.r WARNING @ Tue, 14 Jul 2020 07:58:34: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:58:34: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Tue, 14 Jul 2020 07:58:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:58:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:58:39: 22000000 INFO @ Tue, 14 Jul 2020 07:58:45: 23000000 INFO @ Tue, 14 Jul 2020 07:58:47: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:58:47: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:58:47: #1 total tags in treatment: 10535154 INFO @ Tue, 14 Jul 2020 07:58:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:58:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:58:48: #1 tags after filtering in treatment: 9516013 INFO @ Tue, 14 Jul 2020 07:58:48: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:58:48: #1 finished! INFO @ Tue, 14 Jul 2020 07:58:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:58:48: #2 number of paired peaks: 122 WARNING @ Tue, 14 Jul 2020 07:58:48: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 14 Jul 2020 07:58:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:58:48: start X-correlation... INFO @ Tue, 14 Jul 2020 07:58:48: end of X-cor INFO @ Tue, 14 Jul 2020 07:58:48: #2 finished! INFO @ Tue, 14 Jul 2020 07:58:48: #2 predicted fragment length is 127 bps INFO @ Tue, 14 Jul 2020 07:58:48: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 14 Jul 2020 07:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.20_model.r WARNING @ Tue, 14 Jul 2020 07:58:48: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:58:48: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Tue, 14 Jul 2020 07:58:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:58:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:58:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.10_summits.bed INFO @ Tue, 14 Jul 2020 07:59:03: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (877 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:59:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:59:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:59:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:59:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736478/SRX5736478.20_summits.bed INFO @ Tue, 14 Jul 2020 07:59:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 1 millis CompletedMACS2peakCalling