Job ID = 14168227 SRX = SRX7175256 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6215133 spots for SRR10485696/SRR10485696.sra Written 6215133 spots for SRR10485696/SRR10485696.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169072 ("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: 00:12:50 6215133 reads; of these: 6215133 (100.00%) were paired; of these: 287878 (4.63%) aligned concordantly 0 times 4193363 (67.47%) aligned concordantly exactly 1 time 1733892 (27.90%) aligned concordantly >1 times ---- 287878 pairs aligned concordantly 0 times; of these: 31157 (10.82%) aligned discordantly 1 time ---- 256721 pairs aligned 0 times concordantly or discordantly; of these: 513442 mates make up the pairs; of these: 307931 (59.97%) aligned 0 times 127178 (24.77%) aligned exactly 1 time 78333 (15.26%) aligned >1 times 97.52% overall alignment rate Time searching: 00:12:51 Overall time: 00:12:51 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 8 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] 120327 / 5948756 = 0.0202 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 @ Fri, 10 Dec 2021 16:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.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 @ Fri, 10 Dec 2021 16:32:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:32:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:32:14: 1000000 INFO @ Fri, 10 Dec 2021 16:32:20: 2000000 INFO @ Fri, 10 Dec 2021 16:32:26: 3000000 INFO @ Fri, 10 Dec 2021 16:32:32: 4000000 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 @ Fri, 10 Dec 2021 16:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.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 @ Fri, 10 Dec 2021 16:32:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:32:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:32:38: 5000000 INFO @ Fri, 10 Dec 2021 16:32:44: 1000000 INFO @ Fri, 10 Dec 2021 16:32:45: 6000000 INFO @ Fri, 10 Dec 2021 16:32:52: 2000000 INFO @ Fri, 10 Dec 2021 16:32:53: 7000000 INFO @ Fri, 10 Dec 2021 16:33:00: 3000000 INFO @ Fri, 10 Dec 2021 16:33:00: 8000000 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 @ Fri, 10 Dec 2021 16:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.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 @ Fri, 10 Dec 2021 16:33:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:33:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:33:07: 9000000 INFO @ Fri, 10 Dec 2021 16:33:08: 4000000 INFO @ Fri, 10 Dec 2021 16:33:14: 1000000 INFO @ Fri, 10 Dec 2021 16:33:15: 10000000 INFO @ Fri, 10 Dec 2021 16:33:16: 5000000 INFO @ Fri, 10 Dec 2021 16:33:22: 2000000 INFO @ Fri, 10 Dec 2021 16:33:23: 11000000 INFO @ Fri, 10 Dec 2021 16:33:24: 6000000 INFO @ Fri, 10 Dec 2021 16:33:29: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:33:29: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:33:29: #1 total tags in treatment: 5807177 INFO @ Fri, 10 Dec 2021 16:33:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:33:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:33:29: #1 tags after filtering in treatment: 5545977 INFO @ Fri, 10 Dec 2021 16:33:29: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 16:33:29: #1 finished! INFO @ Fri, 10 Dec 2021 16:33:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:33:30: 3000000 INFO @ Fri, 10 Dec 2021 16:33:30: #2 number of paired peaks: 127 WARNING @ Fri, 10 Dec 2021 16:33:30: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 10 Dec 2021 16:33:30: start model_add_line... INFO @ Fri, 10 Dec 2021 16:33:30: start X-correlation... INFO @ Fri, 10 Dec 2021 16:33:30: end of X-cor INFO @ Fri, 10 Dec 2021 16:33:30: #2 finished! INFO @ Fri, 10 Dec 2021 16:33:30: #2 predicted fragment length is 115 bps INFO @ Fri, 10 Dec 2021 16:33:30: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 10 Dec 2021 16:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.05_model.r WARNING @ Fri, 10 Dec 2021 16:33:30: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:33:30: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Fri, 10 Dec 2021 16:33:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:33:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:33:33: 7000000 INFO @ Fri, 10 Dec 2021 16:33:37: 4000000 INFO @ Fri, 10 Dec 2021 16:33:41: 8000000 INFO @ Fri, 10 Dec 2021 16:33:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:33:45: 5000000 INFO @ Fri, 10 Dec 2021 16:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.05_summits.bed INFO @ Fri, 10 Dec 2021 16:33:47: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (595 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:33:49: 9000000 INFO @ Fri, 10 Dec 2021 16:33:53: 6000000 INFO @ Fri, 10 Dec 2021 16:33:57: 10000000 INFO @ Fri, 10 Dec 2021 16:34:01: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:34:05: 11000000 INFO @ Fri, 10 Dec 2021 16:34:09: 8000000 INFO @ Fri, 10 Dec 2021 16:34:13: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:34:13: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:34:13: #1 total tags in treatment: 5807177 INFO @ Fri, 10 Dec 2021 16:34:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:34:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:34:13: #1 tags after filtering in treatment: 5545977 INFO @ Fri, 10 Dec 2021 16:34:13: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 16:34:13: #1 finished! INFO @ Fri, 10 Dec 2021 16:34:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:34:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:34:13: #2 number of paired peaks: 127 WARNING @ Fri, 10 Dec 2021 16:34:13: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 10 Dec 2021 16:34:13: start model_add_line... INFO @ Fri, 10 Dec 2021 16:34:13: start X-correlation... INFO @ Fri, 10 Dec 2021 16:34:13: end of X-cor INFO @ Fri, 10 Dec 2021 16:34:13: #2 finished! INFO @ Fri, 10 Dec 2021 16:34:13: #2 predicted fragment length is 115 bps INFO @ Fri, 10 Dec 2021 16:34:13: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 10 Dec 2021 16:34:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.10_model.r WARNING @ Fri, 10 Dec 2021 16:34:13: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:34:13: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Fri, 10 Dec 2021 16:34:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:34:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:34:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:34:17: 9000000 INFO @ Fri, 10 Dec 2021 16:34:23: 10000000 INFO @ Fri, 10 Dec 2021 16:34:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:34:30: 11000000 INFO @ Fri, 10 Dec 2021 16:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.10_summits.bed INFO @ Fri, 10 Dec 2021 16:34:30: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (312 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:34:36: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 16:34:36: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 16:34:36: #1 total tags in treatment: 5807177 INFO @ Fri, 10 Dec 2021 16:34:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:34:36: #1 tags after filtering in treatment: 5545977 INFO @ Fri, 10 Dec 2021 16:34:36: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 16:34:36: #1 finished! INFO @ Fri, 10 Dec 2021 16:34:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:34:36: #2 number of paired peaks: 127 WARNING @ Fri, 10 Dec 2021 16:34:36: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Fri, 10 Dec 2021 16:34:36: start model_add_line... INFO @ Fri, 10 Dec 2021 16:34:36: start X-correlation... INFO @ Fri, 10 Dec 2021 16:34:36: end of X-cor INFO @ Fri, 10 Dec 2021 16:34:36: #2 finished! INFO @ Fri, 10 Dec 2021 16:34:36: #2 predicted fragment length is 115 bps INFO @ Fri, 10 Dec 2021 16:34:36: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 10 Dec 2021 16:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.20_model.r WARNING @ Fri, 10 Dec 2021 16:34:36: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:34:36: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Fri, 10 Dec 2021 16:34:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:34:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:34:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7175256/SRX7175256.20_summits.bed INFO @ Fri, 10 Dec 2021 16:34:54: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 1 millis CompletedMACS2peakCalling