Job ID = 14168881 SRX = ERX3978899 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15429384 spots for ERR3975968/ERR3975968.sra Written 15429384 spots for ERR3975968/ERR3975968.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170040 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:13:43 15429384 reads; of these: 15429384 (100.00%) were paired; of these: 5883365 (38.13%) aligned concordantly 0 times 7436905 (48.20%) aligned concordantly exactly 1 time 2109114 (13.67%) aligned concordantly >1 times ---- 5883365 pairs aligned concordantly 0 times; of these: 424985 (7.22%) aligned discordantly 1 time ---- 5458380 pairs aligned 0 times concordantly or discordantly; of these: 10916760 mates make up the pairs; of these: 5562287 (50.95%) aligned 0 times 3370091 (30.87%) aligned exactly 1 time 1984382 (18.18%) aligned >1 times 81.98% overall alignment rate Time searching: 01:13:44 Overall time: 01:13:44 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] 7431406 / 9842771 = 0.7550 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 22:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.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 22:55:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:55:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:55:58: 1000000 INFO @ Fri, 10 Dec 2021 22:56:06: 2000000 INFO @ Fri, 10 Dec 2021 22:56:14: 3000000 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 22:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.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 22:56:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:56:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:56:23: 4000000 INFO @ Fri, 10 Dec 2021 22:56:27: 1000000 INFO @ Fri, 10 Dec 2021 22:56:31: 5000000 INFO @ Fri, 10 Dec 2021 22:56:35: 2000000 INFO @ Fri, 10 Dec 2021 22:56:39: 6000000 INFO @ Fri, 10 Dec 2021 22:56:44: 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 22:56:48: 7000000 INFO @ Fri, 10 Dec 2021 22:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.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 22:56:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:56:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:56:52: 4000000 INFO @ Fri, 10 Dec 2021 22:56:57: 8000000 INFO @ Fri, 10 Dec 2021 22:57:00: 1000000 INFO @ Fri, 10 Dec 2021 22:57:01: 5000000 INFO @ Fri, 10 Dec 2021 22:57:06: 9000000 INFO @ Fri, 10 Dec 2021 22:57:09: 6000000 INFO @ Fri, 10 Dec 2021 22:57:11: 2000000 INFO @ Fri, 10 Dec 2021 22:57:15: 10000000 INFO @ Fri, 10 Dec 2021 22:57:19: 7000000 INFO @ Fri, 10 Dec 2021 22:57:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 22:57:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 22:57:19: #1 total tags in treatment: 2373731 INFO @ Fri, 10 Dec 2021 22:57:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:57:19: #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 22:57:19: #1 tags after filtering in treatment: 2189054 INFO @ Fri, 10 Dec 2021 22:57:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 22:57:19: #1 finished! INFO @ Fri, 10 Dec 2021 22:57:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:57:19: #2 number of paired peaks: 1273 INFO @ Fri, 10 Dec 2021 22:57:19: start model_add_line... INFO @ Fri, 10 Dec 2021 22:57:20: start X-correlation... INFO @ Fri, 10 Dec 2021 22:57:20: end of X-cor INFO @ Fri, 10 Dec 2021 22:57:20: #2 finished! INFO @ Fri, 10 Dec 2021 22:57:20: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Dec 2021 22:57:20: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Dec 2021 22:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.05_model.r WARNING @ Fri, 10 Dec 2021 22:57:20: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:57:20: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 10 Dec 2021 22:57:20: #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 22:57:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:57:21: 3000000 INFO @ Fri, 10 Dec 2021 22:57:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:57:27: 8000000 INFO @ Fri, 10 Dec 2021 22:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.05_summits.bed INFO @ Fri, 10 Dec 2021 22:57:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1990 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:57:31: 4000000 INFO @ Fri, 10 Dec 2021 22:57:36: 9000000 INFO @ Fri, 10 Dec 2021 22:57:41: 5000000 INFO @ Fri, 10 Dec 2021 22:57:44: 10000000 INFO @ Fri, 10 Dec 2021 22:57:48: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 22:57:48: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 22:57:48: #1 total tags in treatment: 2373731 INFO @ Fri, 10 Dec 2021 22:57:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:57:48: #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 22:57:48: #1 tags after filtering in treatment: 2189054 INFO @ Fri, 10 Dec 2021 22:57:48: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 22:57:48: #1 finished! INFO @ Fri, 10 Dec 2021 22:57:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:57:48: #2 number of paired peaks: 1273 INFO @ Fri, 10 Dec 2021 22:57:48: start model_add_line... INFO @ Fri, 10 Dec 2021 22:57:48: start X-correlation... INFO @ Fri, 10 Dec 2021 22:57:48: end of X-cor INFO @ Fri, 10 Dec 2021 22:57:48: #2 finished! INFO @ Fri, 10 Dec 2021 22:57:48: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Dec 2021 22:57:48: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Dec 2021 22:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.10_model.r WARNING @ Fri, 10 Dec 2021 22:57:48: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:57:48: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 10 Dec 2021 22:57:48: #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 22:57:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:57:51: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:57:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:57:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:57:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:57:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.10_summits.bed INFO @ Fri, 10 Dec 2021 22:57:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (760 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:58:01: 7000000 INFO @ Fri, 10 Dec 2021 22:58:11: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:58:21: 9000000 INFO @ Fri, 10 Dec 2021 22:58:31: 10000000 INFO @ Fri, 10 Dec 2021 22:58:35: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 22:58:35: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 22:58:35: #1 total tags in treatment: 2373731 INFO @ Fri, 10 Dec 2021 22:58:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:58:35: #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 22:58:35: #1 tags after filtering in treatment: 2189054 INFO @ Fri, 10 Dec 2021 22:58:35: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 22:58:35: #1 finished! INFO @ Fri, 10 Dec 2021 22:58:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:58:35: #2 number of paired peaks: 1273 INFO @ Fri, 10 Dec 2021 22:58:35: start model_add_line... INFO @ Fri, 10 Dec 2021 22:58:35: start X-correlation... INFO @ Fri, 10 Dec 2021 22:58:35: end of X-cor INFO @ Fri, 10 Dec 2021 22:58:35: #2 finished! INFO @ Fri, 10 Dec 2021 22:58:35: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Dec 2021 22:58:35: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Dec 2021 22:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.20_model.r WARNING @ Fri, 10 Dec 2021 22:58:35: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:58:35: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 10 Dec 2021 22:58:35: #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 22:58:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:58:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:58:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:58:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:58:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978899/ERX3978899.20_summits.bed INFO @ Fri, 10 Dec 2021 22:58:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling