Job ID = 14170308 SRX = SRX8556396 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28019098 spots for SRR12024952/SRR12024952.sra Written 28019098 spots for SRR12024952/SRR12024952.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170780 ("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: 00:19:03 28019098 reads; of these: 28019098 (100.00%) were paired; of these: 26611952 (94.98%) aligned concordantly 0 times 1018513 (3.64%) aligned concordantly exactly 1 time 388633 (1.39%) aligned concordantly >1 times ---- 26611952 pairs aligned concordantly 0 times; of these: 171943 (0.65%) aligned discordantly 1 time ---- 26440009 pairs aligned 0 times concordantly or discordantly; of these: 52880018 mates make up the pairs; of these: 52359197 (99.02%) aligned 0 times 283681 (0.54%) aligned exactly 1 time 237140 (0.45%) aligned >1 times 6.57% overall alignment rate Time searching: 00:19:03 Overall time: 00:19:03 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] 1109801 / 1559341 = 0.7117 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 06:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.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 06:37:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:37:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:06: 1000000 INFO @ Sat, 11 Dec 2021 06:38:10: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:38:10: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:38:10: #1 total tags in treatment: 390793 INFO @ Sat, 11 Dec 2021 06:38:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:38:10: #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 06:38:10: #1 tags after filtering in treatment: 342162 INFO @ Sat, 11 Dec 2021 06:38:10: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:38:10: #1 finished! INFO @ Sat, 11 Dec 2021 06:38:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:38:10: #2 number of paired peaks: 2420 INFO @ Sat, 11 Dec 2021 06:38:10: start model_add_line... INFO @ Sat, 11 Dec 2021 06:38:10: start X-correlation... INFO @ Sat, 11 Dec 2021 06:38:10: end of X-cor INFO @ Sat, 11 Dec 2021 06:38:10: #2 finished! INFO @ Sat, 11 Dec 2021 06:38:10: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 06:38:10: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Dec 2021 06:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.05_model.r WARNING @ Sat, 11 Dec 2021 06:38:10: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:38:10: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 11 Dec 2021 06:38:10: #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 06:38:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:38:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:38:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:38:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.05_summits.bed INFO @ Sat, 11 Dec 2021 06:38:11: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 2 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 06:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.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 06:38:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:35: 1000000 INFO @ Sat, 11 Dec 2021 06:38:39: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:38:39: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:38:39: #1 total tags in treatment: 390793 INFO @ Sat, 11 Dec 2021 06:38:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:38:39: #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 06:38:39: #1 tags after filtering in treatment: 342162 INFO @ Sat, 11 Dec 2021 06:38:39: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:38:39: #1 finished! INFO @ Sat, 11 Dec 2021 06:38:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:38:39: #2 number of paired peaks: 2420 INFO @ Sat, 11 Dec 2021 06:38:39: start model_add_line... INFO @ Sat, 11 Dec 2021 06:38:39: start X-correlation... INFO @ Sat, 11 Dec 2021 06:38:39: end of X-cor INFO @ Sat, 11 Dec 2021 06:38:39: #2 finished! INFO @ Sat, 11 Dec 2021 06:38:39: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 06:38:39: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Dec 2021 06:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.10_model.r WARNING @ Sat, 11 Dec 2021 06:38:39: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:38:39: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 11 Dec 2021 06:38:39: #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 06:38:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:38:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:38:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:38:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:38:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.10_summits.bed INFO @ Sat, 11 Dec 2021 06:38:41: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (371 records, 4 fields): 4 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 06:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.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 06:38:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:05: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:39:09: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:39:09: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:39:09: #1 total tags in treatment: 390793 INFO @ Sat, 11 Dec 2021 06:39:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:39:09: #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 06:39:09: #1 tags after filtering in treatment: 342162 INFO @ Sat, 11 Dec 2021 06:39:09: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 06:39:09: #1 finished! INFO @ Sat, 11 Dec 2021 06:39:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:39:09: #2 number of paired peaks: 2420 INFO @ Sat, 11 Dec 2021 06:39:09: start model_add_line... INFO @ Sat, 11 Dec 2021 06:39:09: start X-correlation... INFO @ Sat, 11 Dec 2021 06:39:09: end of X-cor INFO @ Sat, 11 Dec 2021 06:39:09: #2 finished! INFO @ Sat, 11 Dec 2021 06:39:09: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 06:39:09: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Dec 2021 06:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.20_model.r WARNING @ Sat, 11 Dec 2021 06:39:09: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:39:09: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 11 Dec 2021 06:39:09: #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 06:39:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:39:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:39:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:39:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.20_peaks.narrowPeak BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:39:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556396/SRX8556396.20_summits.bed INFO @ Sat, 11 Dec 2021 06:39:10: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling