Job ID = 14168344 SRX = ERX3978858 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24080274 spots for ERR3975927/ERR3975927.sra Written 24080274 spots for ERR3975927/ERR3975927.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169661 ("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: 01:10:35 24080274 reads; of these: 24080274 (100.00%) were paired; of these: 3399922 (14.12%) aligned concordantly 0 times 15530605 (64.50%) aligned concordantly exactly 1 time 5149747 (21.39%) aligned concordantly >1 times ---- 3399922 pairs aligned concordantly 0 times; of these: 545073 (16.03%) aligned discordantly 1 time ---- 2854849 pairs aligned 0 times concordantly or discordantly; of these: 5709698 mates make up the pairs; of these: 2759559 (48.33%) aligned 0 times 1308054 (22.91%) aligned exactly 1 time 1642085 (28.76%) aligned >1 times 94.27% overall alignment rate Time searching: 01:10:35 Overall time: 01:10:35 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] 14302271 / 21058456 = 0.6792 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 19:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.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 19:13:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:13:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:13:59: 1000000 INFO @ Fri, 10 Dec 2021 19:14:06: 2000000 INFO @ Fri, 10 Dec 2021 19:14:12: 3000000 INFO @ Fri, 10 Dec 2021 19:14:18: 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 19:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.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 19:14:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:14:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:14:24: 5000000 INFO @ Fri, 10 Dec 2021 19:14:29: 1000000 INFO @ Fri, 10 Dec 2021 19:14:30: 6000000 INFO @ Fri, 10 Dec 2021 19:14:36: 2000000 INFO @ Fri, 10 Dec 2021 19:14:36: 7000000 INFO @ Fri, 10 Dec 2021 19:14:42: 3000000 INFO @ Fri, 10 Dec 2021 19:14:42: 8000000 INFO @ Fri, 10 Dec 2021 19:14:48: 4000000 INFO @ Fri, 10 Dec 2021 19:14:48: 9000000 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 19:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.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 19:14:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:14:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:14:54: 5000000 INFO @ Fri, 10 Dec 2021 19:14:54: 10000000 INFO @ Fri, 10 Dec 2021 19:15:00: 1000000 INFO @ Fri, 10 Dec 2021 19:15:01: 6000000 INFO @ Fri, 10 Dec 2021 19:15:01: 11000000 INFO @ Fri, 10 Dec 2021 19:15:07: 2000000 INFO @ Fri, 10 Dec 2021 19:15:07: 7000000 INFO @ Fri, 10 Dec 2021 19:15:07: 12000000 INFO @ Fri, 10 Dec 2021 19:15:13: 8000000 INFO @ Fri, 10 Dec 2021 19:15:13: 13000000 INFO @ Fri, 10 Dec 2021 19:15:14: 3000000 INFO @ Fri, 10 Dec 2021 19:15:19: 9000000 INFO @ Fri, 10 Dec 2021 19:15:20: 14000000 INFO @ Fri, 10 Dec 2021 19:15:21: 4000000 INFO @ Fri, 10 Dec 2021 19:15:26: 10000000 INFO @ Fri, 10 Dec 2021 19:15:26: 15000000 INFO @ Fri, 10 Dec 2021 19:15:28: 5000000 INFO @ Fri, 10 Dec 2021 19:15:32: 11000000 INFO @ Fri, 10 Dec 2021 19:15:32: 16000000 INFO @ Fri, 10 Dec 2021 19:15:35: 6000000 INFO @ Fri, 10 Dec 2021 19:15:38: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:15:38: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:15:38: #1 total tags in treatment: 6701578 INFO @ Fri, 10 Dec 2021 19:15:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:15:38: #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 19:15:38: #1 tags after filtering in treatment: 6204896 INFO @ Fri, 10 Dec 2021 19:15:38: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 19:15:38: #1 finished! INFO @ Fri, 10 Dec 2021 19:15:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:15:38: #2 number of paired peaks: 1235 INFO @ Fri, 10 Dec 2021 19:15:38: start model_add_line... INFO @ Fri, 10 Dec 2021 19:15:38: start X-correlation... INFO @ Fri, 10 Dec 2021 19:15:38: end of X-cor INFO @ Fri, 10 Dec 2021 19:15:38: #2 finished! INFO @ Fri, 10 Dec 2021 19:15:38: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 19:15:38: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 19:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.05_model.r WARNING @ Fri, 10 Dec 2021 19:15:38: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:15:38: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 19:15:38: #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 19:15:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:15:39: 12000000 INFO @ Fri, 10 Dec 2021 19:15:42: 7000000 INFO @ Fri, 10 Dec 2021 19:15:45: 13000000 INFO @ Fri, 10 Dec 2021 19:15:49: 8000000 INFO @ Fri, 10 Dec 2021 19:15:51: 14000000 INFO @ Fri, 10 Dec 2021 19:15:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:15:55: 9000000 INFO @ Fri, 10 Dec 2021 19:15:58: 15000000 INFO @ Fri, 10 Dec 2021 19:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.05_summits.bed INFO @ Fri, 10 Dec 2021 19:15:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9648 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:16:02: 10000000 INFO @ Fri, 10 Dec 2021 19:16:04: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:16:09: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:16:09: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:16:09: #1 total tags in treatment: 6701578 INFO @ Fri, 10 Dec 2021 19:16:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:16:09: #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 19:16:09: #1 tags after filtering in treatment: 6204896 INFO @ Fri, 10 Dec 2021 19:16:09: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 19:16:09: #1 finished! INFO @ Fri, 10 Dec 2021 19:16:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:16:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:16:09: 11000000 INFO @ Fri, 10 Dec 2021 19:16:10: #2 number of paired peaks: 1235 INFO @ Fri, 10 Dec 2021 19:16:10: start model_add_line... INFO @ Fri, 10 Dec 2021 19:16:10: start X-correlation... INFO @ Fri, 10 Dec 2021 19:16:10: end of X-cor INFO @ Fri, 10 Dec 2021 19:16:10: #2 finished! INFO @ Fri, 10 Dec 2021 19:16:10: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 19:16:10: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 19:16:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.10_model.r WARNING @ Fri, 10 Dec 2021 19:16:10: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:16:10: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 19:16:10: #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 19:16:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:16:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:16:16: 12000000 INFO @ Fri, 10 Dec 2021 19:16:22: 13000000 INFO @ Fri, 10 Dec 2021 19:16:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:16:28: 14000000 INFO @ Fri, 10 Dec 2021 19:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.10_summits.bed INFO @ Fri, 10 Dec 2021 19:16:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5129 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:16:34: 15000000 INFO @ Fri, 10 Dec 2021 19:16:41: 16000000 INFO @ Fri, 10 Dec 2021 19:16:46: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 19:16:46: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 19:16:46: #1 total tags in treatment: 6701578 INFO @ Fri, 10 Dec 2021 19:16:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:16:46: #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 19:16:46: #1 tags after filtering in treatment: 6204896 INFO @ Fri, 10 Dec 2021 19:16:46: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 19:16:46: #1 finished! INFO @ Fri, 10 Dec 2021 19:16:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:16:46: #2 number of paired peaks: 1235 INFO @ Fri, 10 Dec 2021 19:16:46: start model_add_line... INFO @ Fri, 10 Dec 2021 19:16:46: start X-correlation... INFO @ Fri, 10 Dec 2021 19:16:46: end of X-cor INFO @ Fri, 10 Dec 2021 19:16:46: #2 finished! INFO @ Fri, 10 Dec 2021 19:16:46: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 19:16:46: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 19:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.20_model.r WARNING @ Fri, 10 Dec 2021 19:16:46: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:16:46: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 19:16:46: #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 19:16:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:16:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978858/ERX3978858.20_summits.bed INFO @ Fri, 10 Dec 2021 19:17:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1840 records, 4 fields): 3 millis CompletedMACS2peakCalling