Job ID = 14168445 SRX = ERX3978867 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10201048 spots for ERR3975936/ERR3975936.sra Written 10201048 spots for ERR3975936/ERR3975936.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169668 ("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: 00:42:06 10201048 reads; of these: 10201048 (100.00%) were paired; of these: 3722284 (36.49%) aligned concordantly 0 times 4887102 (47.91%) aligned concordantly exactly 1 time 1591662 (15.60%) aligned concordantly >1 times ---- 3722284 pairs aligned concordantly 0 times; of these: 459145 (12.34%) aligned discordantly 1 time ---- 3263139 pairs aligned 0 times concordantly or discordantly; of these: 6526278 mates make up the pairs; of these: 3275808 (50.19%) aligned 0 times 1844535 (28.26%) aligned exactly 1 time 1405935 (21.54%) aligned >1 times 83.94% overall alignment rate Time searching: 00:42:06 Overall time: 00:42:06 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 8 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] 5481936 / 6820775 = 0.8037 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 19:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.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 19:13:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:13:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:13:52: 1000000 INFO @ Fri, 10 Dec 2021 19:13:58: 2000000 INFO @ Fri, 10 Dec 2021 19:14:03: 3000000 INFO @ Fri, 10 Dec 2021 19:14:08: 4000000 INFO @ Fri, 10 Dec 2021 19:14:14: 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 19:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.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 19:14:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:14:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:14:20: 6000000 INFO @ Fri, 10 Dec 2021 19:14:21: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:14:21: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:14:21: #1 total tags in treatment: 1320019 INFO @ Fri, 10 Dec 2021 19:14:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:14:21: #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 19:14:21: #1 tags after filtering in treatment: 1123876 INFO @ Fri, 10 Dec 2021 19:14:21: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:14:21: #1 finished! INFO @ Fri, 10 Dec 2021 19:14:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:14:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:14:21: #2 number of paired peaks: 3029 INFO @ Fri, 10 Dec 2021 19:14:21: start model_add_line... INFO @ Fri, 10 Dec 2021 19:14:21: start X-correlation... INFO @ Fri, 10 Dec 2021 19:14:21: end of X-cor INFO @ Fri, 10 Dec 2021 19:14:21: #2 finished! INFO @ Fri, 10 Dec 2021 19:14:21: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 19:14:21: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Dec 2021 19:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.05_model.r WARNING @ Fri, 10 Dec 2021 19:14:21: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:14:21: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Dec 2021 19:14:21: #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 19:14:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:14:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.05_summits.bed INFO @ Fri, 10 Dec 2021 19:14:25: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2110 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:14:25: 1000000 INFO @ Fri, 10 Dec 2021 19:14:33: 2000000 INFO @ Fri, 10 Dec 2021 19:14:41: 3000000 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 19:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.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 19:14:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:14:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:14:50: 4000000 INFO @ Fri, 10 Dec 2021 19:14:53: 1000000 INFO @ Fri, 10 Dec 2021 19:14:58: 5000000 INFO @ Fri, 10 Dec 2021 19:15:00: 2000000 INFO @ Fri, 10 Dec 2021 19:15:04: 6000000 INFO @ Fri, 10 Dec 2021 19:15:05: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:15:05: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:15:05: #1 total tags in treatment: 1320019 INFO @ Fri, 10 Dec 2021 19:15:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:15:05: #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 19:15:05: #1 tags after filtering in treatment: 1123876 INFO @ Fri, 10 Dec 2021 19:15:05: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:15:05: #1 finished! INFO @ Fri, 10 Dec 2021 19:15:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:15:06: #2 number of paired peaks: 3029 INFO @ Fri, 10 Dec 2021 19:15:06: start model_add_line... INFO @ Fri, 10 Dec 2021 19:15:06: start X-correlation... INFO @ Fri, 10 Dec 2021 19:15:06: end of X-cor INFO @ Fri, 10 Dec 2021 19:15:06: #2 finished! INFO @ Fri, 10 Dec 2021 19:15:06: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 19:15:06: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Dec 2021 19:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.10_model.r WARNING @ Fri, 10 Dec 2021 19:15:06: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:15:06: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Dec 2021 19:15:06: #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 19:15:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:15:07: 3000000 INFO @ Fri, 10 Dec 2021 19:15:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.10_summits.bed INFO @ Fri, 10 Dec 2021 19:15:10: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (815 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:15:12: 4000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:15:18: 5000000 INFO @ Fri, 10 Dec 2021 19:15:23: 6000000 INFO @ Fri, 10 Dec 2021 19:15:24: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:15:24: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:15:24: #1 total tags in treatment: 1320019 INFO @ Fri, 10 Dec 2021 19:15:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:15:24: #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 19:15:24: #1 tags after filtering in treatment: 1123876 INFO @ Fri, 10 Dec 2021 19:15:24: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:15:24: #1 finished! INFO @ Fri, 10 Dec 2021 19:15:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:15:24: #2 number of paired peaks: 3029 INFO @ Fri, 10 Dec 2021 19:15:24: start model_add_line... INFO @ Fri, 10 Dec 2021 19:15:24: start X-correlation... INFO @ Fri, 10 Dec 2021 19:15:24: end of X-cor INFO @ Fri, 10 Dec 2021 19:15:24: #2 finished! INFO @ Fri, 10 Dec 2021 19:15:24: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 19:15:24: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Dec 2021 19:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.20_model.r WARNING @ Fri, 10 Dec 2021 19:15:24: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:15:24: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Dec 2021 19:15:24: #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 19:15:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:15:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978867/ERX3978867.20_summits.bed INFO @ Fri, 10 Dec 2021 19:15:28: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 8 millis CompletedMACS2peakCalling