Job ID = 14168040 SRX = ERX3978935 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22728611 spots for ERR3976005/ERR3976005.sra Written 22728611 spots for ERR3976005/ERR3976005.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168928 ("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: 00:57:09 22728611 reads; of these: 22728611 (100.00%) were paired; of these: 2792445 (12.29%) aligned concordantly 0 times 15877709 (69.86%) aligned concordantly exactly 1 time 4058457 (17.86%) aligned concordantly >1 times ---- 2792445 pairs aligned concordantly 0 times; of these: 574630 (20.58%) aligned discordantly 1 time ---- 2217815 pairs aligned 0 times concordantly or discordantly; of these: 4435630 mates make up the pairs; of these: 2347152 (52.92%) aligned 0 times 1125449 (25.37%) aligned exactly 1 time 963029 (21.71%) aligned >1 times 94.84% overall alignment rate Time searching: 00:57:10 Overall time: 00:57:10 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 20 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] 13262844 / 20400202 = 0.6501 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 15:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.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 15:48:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:48:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:48:58: 1000000 INFO @ Fri, 10 Dec 2021 15:49:05: 2000000 INFO @ Fri, 10 Dec 2021 15:49:12: 3000000 INFO @ Fri, 10 Dec 2021 15:49:19: 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 15:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.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 15:49:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:49:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:49:25: 5000000 INFO @ Fri, 10 Dec 2021 15:49:29: 1000000 INFO @ Fri, 10 Dec 2021 15:49:33: 6000000 INFO @ Fri, 10 Dec 2021 15:49:36: 2000000 INFO @ Fri, 10 Dec 2021 15:49:40: 7000000 INFO @ Fri, 10 Dec 2021 15:49:43: 3000000 INFO @ Fri, 10 Dec 2021 15:49:47: 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 15:49:49: 4000000 INFO @ Fri, 10 Dec 2021 15:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.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 15:49:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:49:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:49:54: 9000000 INFO @ Fri, 10 Dec 2021 15:49:56: 5000000 INFO @ Fri, 10 Dec 2021 15:49:58: 1000000 INFO @ Fri, 10 Dec 2021 15:50:01: 10000000 INFO @ Fri, 10 Dec 2021 15:50:03: 6000000 INFO @ Fri, 10 Dec 2021 15:50:05: 2000000 INFO @ Fri, 10 Dec 2021 15:50:09: 11000000 INFO @ Fri, 10 Dec 2021 15:50:10: 7000000 INFO @ Fri, 10 Dec 2021 15:50:13: 3000000 INFO @ Fri, 10 Dec 2021 15:50:16: 12000000 INFO @ Fri, 10 Dec 2021 15:50:17: 8000000 INFO @ Fri, 10 Dec 2021 15:50:20: 4000000 INFO @ Fri, 10 Dec 2021 15:50:23: 13000000 INFO @ Fri, 10 Dec 2021 15:50:24: 9000000 INFO @ Fri, 10 Dec 2021 15:50:27: 5000000 INFO @ Fri, 10 Dec 2021 15:50:31: 14000000 INFO @ Fri, 10 Dec 2021 15:50:31: 10000000 INFO @ Fri, 10 Dec 2021 15:50:34: 6000000 INFO @ Fri, 10 Dec 2021 15:50:38: 11000000 INFO @ Fri, 10 Dec 2021 15:50:38: 15000000 INFO @ Fri, 10 Dec 2021 15:50:40: 7000000 INFO @ Fri, 10 Dec 2021 15:50:46: 12000000 INFO @ Fri, 10 Dec 2021 15:50:46: 16000000 INFO @ Fri, 10 Dec 2021 15:50:47: 8000000 INFO @ Fri, 10 Dec 2021 15:50:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:50:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:50:50: #1 total tags in treatment: 7037712 INFO @ Fri, 10 Dec 2021 15:50:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:50:50: #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 15:50:50: #1 tags after filtering in treatment: 6515908 INFO @ Fri, 10 Dec 2021 15:50:50: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 15:50:50: #1 finished! INFO @ Fri, 10 Dec 2021 15:50:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:50:50: #2 number of paired peaks: 1347 INFO @ Fri, 10 Dec 2021 15:50:50: start model_add_line... INFO @ Fri, 10 Dec 2021 15:50:50: start X-correlation... INFO @ Fri, 10 Dec 2021 15:50:50: end of X-cor INFO @ Fri, 10 Dec 2021 15:50:50: #2 finished! INFO @ Fri, 10 Dec 2021 15:50:50: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 15:50:50: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 15:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.05_model.r WARNING @ Fri, 10 Dec 2021 15:50:50: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:50:50: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 15:50:50: #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 15:50:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:50:53: 13000000 INFO @ Fri, 10 Dec 2021 15:50:54: 9000000 INFO @ Fri, 10 Dec 2021 15:51:00: 14000000 INFO @ Fri, 10 Dec 2021 15:51:01: 10000000 INFO @ Fri, 10 Dec 2021 15:51:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:51:07: 15000000 INFO @ Fri, 10 Dec 2021 15:51:07: 11000000 INFO @ Fri, 10 Dec 2021 15:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.05_summits.bed INFO @ Fri, 10 Dec 2021 15:51:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6578 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:51:13: 16000000 INFO @ Fri, 10 Dec 2021 15:51:14: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:51:17: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:51:17: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:51:17: #1 total tags in treatment: 7037712 INFO @ Fri, 10 Dec 2021 15:51:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:51:17: #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 15:51:17: #1 tags after filtering in treatment: 6515908 INFO @ Fri, 10 Dec 2021 15:51:17: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 15:51:17: #1 finished! INFO @ Fri, 10 Dec 2021 15:51:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:51:18: #2 number of paired peaks: 1347 INFO @ Fri, 10 Dec 2021 15:51:18: start model_add_line... INFO @ Fri, 10 Dec 2021 15:51:18: start X-correlation... INFO @ Fri, 10 Dec 2021 15:51:18: end of X-cor INFO @ Fri, 10 Dec 2021 15:51:18: #2 finished! INFO @ Fri, 10 Dec 2021 15:51:18: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 15:51:18: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 15:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.10_model.r WARNING @ Fri, 10 Dec 2021 15:51:18: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:51:18: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 15:51:18: #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 15:51:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:51:21: 13000000 INFO @ Fri, 10 Dec 2021 15:51:27: 14000000 INFO @ Fri, 10 Dec 2021 15:51:33: 15000000 INFO @ Fri, 10 Dec 2021 15:51:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:51:40: 16000000 INFO @ Fri, 10 Dec 2021 15:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.10_summits.bed INFO @ Fri, 10 Dec 2021 15:51:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3098 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:51:43: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:51:43: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:51:43: #1 total tags in treatment: 7037712 INFO @ Fri, 10 Dec 2021 15:51:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:51:43: #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 15:51:43: #1 tags after filtering in treatment: 6515908 INFO @ Fri, 10 Dec 2021 15:51:43: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 15:51:43: #1 finished! INFO @ Fri, 10 Dec 2021 15:51:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:51:44: #2 number of paired peaks: 1347 INFO @ Fri, 10 Dec 2021 15:51:44: start model_add_line... INFO @ Fri, 10 Dec 2021 15:51:44: start X-correlation... INFO @ Fri, 10 Dec 2021 15:51:44: end of X-cor INFO @ Fri, 10 Dec 2021 15:51:44: #2 finished! INFO @ Fri, 10 Dec 2021 15:51:44: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 15:51:44: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 15:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.20_model.r WARNING @ Fri, 10 Dec 2021 15:51:44: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:51:44: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 15:51:44: #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 15:51:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:51:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:51:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978935/ERX3978935.20_summits.bed INFO @ Fri, 10 Dec 2021 15:52:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1252 records, 4 fields): 3 millis CompletedMACS2peakCalling