Job ID = 14171233 SRX = SRX9555338 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2191410 spots for SRR13110857/SRR13110857.sra Written 2191410 spots for SRR13110857/SRR13110857.sra Read 1961412 spots for SRR13110858/SRR13110858.sra Written 1961412 spots for SRR13110858/SRR13110858.sra Read 2002087 spots for SRR13110859/SRR13110859.sra Written 2002087 spots for SRR13110859/SRR13110859.sra Read 1805857 spots for SRR13110860/SRR13110860.sra Written 1805857 spots for SRR13110860/SRR13110860.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171688 ("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: 00:02:09 7960766 reads; of these: 7960766 (100.00%) were paired; of these: 7761894 (97.50%) aligned concordantly 0 times 138099 (1.73%) aligned concordantly exactly 1 time 60773 (0.76%) aligned concordantly >1 times ---- 7761894 pairs aligned concordantly 0 times; of these: 1562 (0.02%) aligned discordantly 1 time ---- 7760332 pairs aligned 0 times concordantly or discordantly; of these: 15520664 mates make up the pairs; of these: 15498617 (99.86%) aligned 0 times 6169 (0.04%) aligned exactly 1 time 15878 (0.10%) aligned >1 times 2.66% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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_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] 1310 / 62249 = 0.0210 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 @ Sat, 11 Dec 2021 10:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.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, 11 Dec 2021 10:42:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:42:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:42:29: #1 tag size is determined as 55 bps INFO @ Sat, 11 Dec 2021 10:42:29: #1 tag size = 55 INFO @ Sat, 11 Dec 2021 10:42:29: #1 total tags in treatment: 197563 INFO @ Sat, 11 Dec 2021 10:42:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:42:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:42:29: #1 tags after filtering in treatment: 192474 INFO @ Sat, 11 Dec 2021 10:42:29: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:42:29: #1 finished! INFO @ Sat, 11 Dec 2021 10:42:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:42:29: #2 number of paired peaks: 2759 INFO @ Sat, 11 Dec 2021 10:42:29: start model_add_line... INFO @ Sat, 11 Dec 2021 10:42:29: start X-correlation... INFO @ Sat, 11 Dec 2021 10:42:29: end of X-cor INFO @ Sat, 11 Dec 2021 10:42:29: #2 finished! INFO @ Sat, 11 Dec 2021 10:42:29: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 10:42:29: #2 alternative fragment length(s) may be 48,140,176,207,230 bps INFO @ Sat, 11 Dec 2021 10:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.05_model.r WARNING @ Sat, 11 Dec 2021 10:42:29: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:42:29: #2 You may need to consider one of the other alternative d(s): 48,140,176,207,230 WARNING @ Sat, 11 Dec 2021 10:42:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:42:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:42:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:42:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:42:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:42:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.05_summits.bed INFO @ Sat, 11 Dec 2021 10:42:30: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 10:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.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, 11 Dec 2021 10:42:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:42:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:42:58: #1 tag size is determined as 55 bps INFO @ Sat, 11 Dec 2021 10:42:58: #1 tag size = 55 INFO @ Sat, 11 Dec 2021 10:42:58: #1 total tags in treatment: 197563 INFO @ Sat, 11 Dec 2021 10:42:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:42:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:42:58: #1 tags after filtering in treatment: 192474 INFO @ Sat, 11 Dec 2021 10:42:58: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:42:58: #1 finished! INFO @ Sat, 11 Dec 2021 10:42:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:42:58: #2 number of paired peaks: 2759 INFO @ Sat, 11 Dec 2021 10:42:58: start model_add_line... INFO @ Sat, 11 Dec 2021 10:42:58: start X-correlation... INFO @ Sat, 11 Dec 2021 10:42:58: end of X-cor INFO @ Sat, 11 Dec 2021 10:42:58: #2 finished! INFO @ Sat, 11 Dec 2021 10:42:58: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 10:42:58: #2 alternative fragment length(s) may be 48,140,176,207,230 bps INFO @ Sat, 11 Dec 2021 10:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.10_model.r WARNING @ Sat, 11 Dec 2021 10:42:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:42:58: #2 You may need to consider one of the other alternative d(s): 48,140,176,207,230 WARNING @ Sat, 11 Dec 2021 10:42:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:42:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:42:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:42:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:42:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.10_summits.bed INFO @ Sat, 11 Dec 2021 10:42:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 28 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 @ Sat, 11 Dec 2021 10:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.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, 11 Dec 2021 10:43:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:43:25: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:43:28: #1 tag size is determined as 55 bps INFO @ Sat, 11 Dec 2021 10:43:28: #1 tag size = 55 INFO @ Sat, 11 Dec 2021 10:43:28: #1 total tags in treatment: 197563 INFO @ Sat, 11 Dec 2021 10:43:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:43:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:43:28: #1 tags after filtering in treatment: 192474 INFO @ Sat, 11 Dec 2021 10:43:28: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:43:28: #1 finished! INFO @ Sat, 11 Dec 2021 10:43:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:43:28: #2 number of paired peaks: 2759 INFO @ Sat, 11 Dec 2021 10:43:28: start model_add_line... INFO @ Sat, 11 Dec 2021 10:43:28: start X-correlation... INFO @ Sat, 11 Dec 2021 10:43:28: end of X-cor INFO @ Sat, 11 Dec 2021 10:43:28: #2 finished! INFO @ Sat, 11 Dec 2021 10:43:28: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 10:43:28: #2 alternative fragment length(s) may be 48,140,176,207,230 bps INFO @ Sat, 11 Dec 2021 10:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.20_model.r WARNING @ Sat, 11 Dec 2021 10:43:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:43:28: #2 You may need to consider one of the other alternative d(s): 48,140,176,207,230 WARNING @ Sat, 11 Dec 2021 10:43:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:43:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:43:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555338/SRX9555338.20_summits.bed INFO @ Sat, 11 Dec 2021 10:43:29: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling