Job ID = 12265318 SRX = SRX5736449 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15311769 spots for SRR8956860/SRR8956860.sra Written 15311769 spots for SRR8956860/SRR8956860.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265555 ("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: 00:27:59 15311769 reads; of these: 15311769 (100.00%) were paired; of these: 6468192 (42.24%) aligned concordantly 0 times 2862270 (18.69%) aligned concordantly exactly 1 time 5981307 (39.06%) aligned concordantly >1 times ---- 6468192 pairs aligned concordantly 0 times; of these: 411928 (6.37%) aligned discordantly 1 time ---- 6056264 pairs aligned 0 times concordantly or discordantly; of these: 12112528 mates make up the pairs; of these: 10728081 (88.57%) aligned 0 times 174371 (1.44%) aligned exactly 1 time 1210076 (9.99%) aligned >1 times 64.97% overall alignment rate Time searching: 00:27:59 Overall time: 00:27:59 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] 4014337 / 9169122 = 0.4378 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 07:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.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 07:11:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:11:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:11:08: 1000000 INFO @ Sat, 03 Apr 2021 07:11:15: 2000000 INFO @ Sat, 03 Apr 2021 07:11:21: 3000000 INFO @ Sat, 03 Apr 2021 07:11:28: 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 07:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.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 07:11:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:11:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:11:34: 5000000 INFO @ Sat, 03 Apr 2021 07:11:38: 1000000 INFO @ Sat, 03 Apr 2021 07:11:39: 6000000 INFO @ Sat, 03 Apr 2021 07:11:44: 2000000 INFO @ Sat, 03 Apr 2021 07:11:45: 7000000 INFO @ Sat, 03 Apr 2021 07:11:51: 8000000 INFO @ Sat, 03 Apr 2021 07:11:51: 3000000 INFO @ Sat, 03 Apr 2021 07:11:56: 9000000 INFO @ Sat, 03 Apr 2021 07:11:57: 4000000 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 07:12:02: 10000000 INFO @ Sat, 03 Apr 2021 07:12:02: 5000000 INFO @ Sat, 03 Apr 2021 07:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.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 07:12:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:12:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:12:08: 6000000 INFO @ Sat, 03 Apr 2021 07:12:09: 11000000 INFO @ Sat, 03 Apr 2021 07:12:09: 1000000 INFO @ Sat, 03 Apr 2021 07:12:14: 7000000 INFO @ Sat, 03 Apr 2021 07:12:15: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:12:15: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:12:15: #1 total tags in treatment: 4863124 INFO @ Sat, 03 Apr 2021 07:12:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:12:15: #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 07:12:15: #1 tags after filtering in treatment: 3532784 INFO @ Sat, 03 Apr 2021 07:12:15: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:12:15: #1 finished! INFO @ Sat, 03 Apr 2021 07:12:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:12:15: #2 number of paired peaks: 891 WARNING @ Sat, 03 Apr 2021 07:12:15: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Sat, 03 Apr 2021 07:12:15: start model_add_line... INFO @ Sat, 03 Apr 2021 07:12:16: start X-correlation... INFO @ Sat, 03 Apr 2021 07:12:16: end of X-cor INFO @ Sat, 03 Apr 2021 07:12:16: #2 finished! INFO @ Sat, 03 Apr 2021 07:12:16: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Apr 2021 07:12:16: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 03 Apr 2021 07:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.05_model.r WARNING @ Sat, 03 Apr 2021 07:12:16: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:12:16: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sat, 03 Apr 2021 07:12:16: #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 07:12:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:12:17: 2000000 INFO @ Sat, 03 Apr 2021 07:12:19: 8000000 INFO @ Sat, 03 Apr 2021 07:12:23: 3000000 INFO @ Sat, 03 Apr 2021 07:12:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:12:26: 9000000 INFO @ Sat, 03 Apr 2021 07:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.05_summits.bed INFO @ Sat, 03 Apr 2021 07:12:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2361 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:12:29: 4000000 INFO @ Sat, 03 Apr 2021 07:12:31: 10000000 INFO @ Sat, 03 Apr 2021 07:12:35: 5000000 INFO @ Sat, 03 Apr 2021 07:12:37: 11000000 INFO @ Sat, 03 Apr 2021 07:12:41: 6000000 INFO @ Sat, 03 Apr 2021 07:12:42: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:12:42: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:12:42: #1 total tags in treatment: 4863124 INFO @ Sat, 03 Apr 2021 07:12:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:12:42: #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 07:12:43: #1 tags after filtering in treatment: 3532784 INFO @ Sat, 03 Apr 2021 07:12:43: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:12:43: #1 finished! INFO @ Sat, 03 Apr 2021 07:12:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:12:43: #2 number of paired peaks: 891 WARNING @ Sat, 03 Apr 2021 07:12:43: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Sat, 03 Apr 2021 07:12:43: start model_add_line... INFO @ Sat, 03 Apr 2021 07:12:43: start X-correlation... INFO @ Sat, 03 Apr 2021 07:12:43: end of X-cor INFO @ Sat, 03 Apr 2021 07:12:43: #2 finished! INFO @ Sat, 03 Apr 2021 07:12:43: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Apr 2021 07:12:43: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 03 Apr 2021 07:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.10_model.r WARNING @ Sat, 03 Apr 2021 07:12:43: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:12:43: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sat, 03 Apr 2021 07:12:43: #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 07:12:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:12:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:12:47: 7000000 INFO @ Sat, 03 Apr 2021 07:12:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:12:53: 8000000 INFO @ Sat, 03 Apr 2021 07:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.10_summits.bed INFO @ Sat, 03 Apr 2021 07:12:54: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1119 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:12:59: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:13:05: 10000000 INFO @ Sat, 03 Apr 2021 07:13:11: 11000000 INFO @ Sat, 03 Apr 2021 07:13:16: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:13:16: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:13:16: #1 total tags in treatment: 4863124 INFO @ Sat, 03 Apr 2021 07:13:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:16: #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 07:13:16: #1 tags after filtering in treatment: 3532784 INFO @ Sat, 03 Apr 2021 07:13:16: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:13:16: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:16: #2 number of paired peaks: 891 WARNING @ Sat, 03 Apr 2021 07:13:16: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:16: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:16: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:16: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:16: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:16: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Apr 2021 07:13:16: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 03 Apr 2021 07:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.20_model.r WARNING @ Sat, 03 Apr 2021 07:13:16: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:16: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sat, 03 Apr 2021 07:13:16: #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 07:13:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:13:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736449/SRX5736449.20_summits.bed INFO @ Sat, 03 Apr 2021 07:13:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。