Job ID = 14168265 SRX = ERX3978842 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15261890 spots for ERR3975911/ERR3975911.sra Written 15261890 spots for ERR3975911/ERR3975911.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169423 ("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: 00:44:11 15261890 reads; of these: 15261890 (100.00%) were paired; of these: 5956386 (39.03%) aligned concordantly 0 times 7328591 (48.02%) aligned concordantly exactly 1 time 1976913 (12.95%) aligned concordantly >1 times ---- 5956386 pairs aligned concordantly 0 times; of these: 852738 (14.32%) aligned discordantly 1 time ---- 5103648 pairs aligned 0 times concordantly or discordantly; of these: 10207296 mates make up the pairs; of these: 5578706 (54.65%) aligned 0 times 2810012 (27.53%) aligned exactly 1 time 1818578 (17.82%) aligned >1 times 81.72% overall alignment rate Time searching: 00:44:11 Overall time: 00:44:11 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] 7564071 / 9966271 = 0.7590 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 17:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.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 17:34:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:34:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:34:46: 1000000 INFO @ Fri, 10 Dec 2021 17:34:51: 2000000 INFO @ Fri, 10 Dec 2021 17:34:56: 3000000 INFO @ Fri, 10 Dec 2021 17:35:00: 4000000 INFO @ Fri, 10 Dec 2021 17:35:05: 5000000 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 17:35:10: 6000000 INFO @ Fri, 10 Dec 2021 17:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.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 17:35:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:35:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:35:15: 7000000 INFO @ Fri, 10 Dec 2021 17:35:16: 1000000 INFO @ Fri, 10 Dec 2021 17:35:20: 8000000 INFO @ Fri, 10 Dec 2021 17:35:21: 2000000 INFO @ Fri, 10 Dec 2021 17:35:25: 9000000 INFO @ Fri, 10 Dec 2021 17:35:26: 3000000 INFO @ Fri, 10 Dec 2021 17:35:29: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:35:29: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:35:29: #1 total tags in treatment: 2290670 INFO @ Fri, 10 Dec 2021 17:35:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:35:29: #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 17:35:29: #1 tags after filtering in treatment: 2119324 INFO @ Fri, 10 Dec 2021 17:35:29: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:35:29: #1 finished! INFO @ Fri, 10 Dec 2021 17:35:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:35:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:35:29: #2 number of paired peaks: 1038 INFO @ Fri, 10 Dec 2021 17:35:29: start model_add_line... INFO @ Fri, 10 Dec 2021 17:35:29: start X-correlation... INFO @ Fri, 10 Dec 2021 17:35:29: end of X-cor INFO @ Fri, 10 Dec 2021 17:35:29: #2 finished! INFO @ Fri, 10 Dec 2021 17:35:29: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Dec 2021 17:35:29: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Dec 2021 17:35:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.05_model.r WARNING @ Fri, 10 Dec 2021 17:35:29: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:35:29: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Fri, 10 Dec 2021 17:35:29: #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 17:35:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:35:31: 4000000 INFO @ Fri, 10 Dec 2021 17:35:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:35:35: 5000000 INFO @ Fri, 10 Dec 2021 17:35:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.05_summits.bed INFO @ Fri, 10 Dec 2021 17:35:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1416 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 17:35:40: 6000000 INFO @ Fri, 10 Dec 2021 17:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.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 17:35:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:35:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:35:45: 7000000 INFO @ Fri, 10 Dec 2021 17:35:46: 1000000 INFO @ Fri, 10 Dec 2021 17:35:50: 8000000 INFO @ Fri, 10 Dec 2021 17:35:51: 2000000 INFO @ Fri, 10 Dec 2021 17:35:55: 9000000 INFO @ Fri, 10 Dec 2021 17:35:56: 3000000 INFO @ Fri, 10 Dec 2021 17:35:59: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:35:59: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:35:59: #1 total tags in treatment: 2290670 INFO @ Fri, 10 Dec 2021 17:35:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:35:59: #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 17:35:59: #1 tags after filtering in treatment: 2119324 INFO @ Fri, 10 Dec 2021 17:35:59: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:35:59: #1 finished! INFO @ Fri, 10 Dec 2021 17:35:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:35:59: #2 number of paired peaks: 1038 INFO @ Fri, 10 Dec 2021 17:35:59: start model_add_line... INFO @ Fri, 10 Dec 2021 17:35:59: start X-correlation... INFO @ Fri, 10 Dec 2021 17:35:59: end of X-cor INFO @ Fri, 10 Dec 2021 17:35:59: #2 finished! INFO @ Fri, 10 Dec 2021 17:35:59: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Dec 2021 17:35:59: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Dec 2021 17:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.10_model.r WARNING @ Fri, 10 Dec 2021 17:35:59: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:35:59: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Fri, 10 Dec 2021 17:35:59: #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 17:35:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:36:00: 4000000 INFO @ Fri, 10 Dec 2021 17:36:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:36:05: 5000000 INFO @ Fri, 10 Dec 2021 17:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.10_summits.bed INFO @ Fri, 10 Dec 2021 17:36:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (632 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:36:10: 6000000 INFO @ Fri, 10 Dec 2021 17:36:15: 7000000 INFO @ Fri, 10 Dec 2021 17:36:20: 8000000 INFO @ Fri, 10 Dec 2021 17:36:26: 9000000 INFO @ Fri, 10 Dec 2021 17:36:29: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:36:29: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:36:29: #1 total tags in treatment: 2290670 INFO @ Fri, 10 Dec 2021 17:36:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:36:29: #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 17:36:29: #1 tags after filtering in treatment: 2119324 INFO @ Fri, 10 Dec 2021 17:36:29: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:36:29: #1 finished! INFO @ Fri, 10 Dec 2021 17:36:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:36:30: #2 number of paired peaks: 1038 INFO @ Fri, 10 Dec 2021 17:36:30: start model_add_line... INFO @ Fri, 10 Dec 2021 17:36:30: start X-correlation... INFO @ Fri, 10 Dec 2021 17:36:30: end of X-cor INFO @ Fri, 10 Dec 2021 17:36:30: #2 finished! INFO @ Fri, 10 Dec 2021 17:36:30: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Dec 2021 17:36:30: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Dec 2021 17:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.20_model.r WARNING @ Fri, 10 Dec 2021 17:36:30: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:36:30: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Fri, 10 Dec 2021 17:36:30: #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 17:36:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:36:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:36:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:36:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:36:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:36:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978842/ERX3978842.20_summits.bed INFO @ Fri, 10 Dec 2021 17:36:37: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。