Job ID = 14158413 SRX = SRX10641196 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21102173 spots for SRR14280082/SRR14280082.sra Written 21102173 spots for SRR14280082/SRR14280082.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159209 ("srTce11") 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: 00:36:13 21102173 reads; of these: 21102173 (100.00%) were paired; of these: 13230984 (62.70%) aligned concordantly 0 times 4715063 (22.34%) aligned concordantly exactly 1 time 3156126 (14.96%) aligned concordantly >1 times ---- 13230984 pairs aligned concordantly 0 times; of these: 1925837 (14.56%) aligned discordantly 1 time ---- 11305147 pairs aligned 0 times concordantly or discordantly; of these: 22610294 mates make up the pairs; of these: 21615388 (95.60%) aligned 0 times 482211 (2.13%) aligned exactly 1 time 512695 (2.27%) aligned >1 times 48.78% overall alignment rate Time searching: 00:36:13 Overall time: 00:36:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 2226688 / 9750312 = 0.2284 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 @ Wed, 08 Dec 2021 18:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 18:19:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:19:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:19:40: 1000000 INFO @ Wed, 08 Dec 2021 18:19:46: 2000000 INFO @ Wed, 08 Dec 2021 18:19:52: 3000000 INFO @ Wed, 08 Dec 2021 18:19:59: 4000000 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 @ Wed, 08 Dec 2021 18:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 18:20:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:20:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:20:05: 5000000 INFO @ Wed, 08 Dec 2021 18:20:11: 1000000 INFO @ Wed, 08 Dec 2021 18:20:12: 6000000 INFO @ Wed, 08 Dec 2021 18:20:19: 7000000 INFO @ Wed, 08 Dec 2021 18:20:19: 2000000 INFO @ Wed, 08 Dec 2021 18:20:25: 8000000 INFO @ Wed, 08 Dec 2021 18:20:27: 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 @ Wed, 08 Dec 2021 18:20:32: 9000000 INFO @ Wed, 08 Dec 2021 18:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 18:20:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:20:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:20:35: 4000000 INFO @ Wed, 08 Dec 2021 18:20:39: 10000000 INFO @ Wed, 08 Dec 2021 18:20:42: 1000000 INFO @ Wed, 08 Dec 2021 18:20:43: 5000000 INFO @ Wed, 08 Dec 2021 18:20:46: 11000000 INFO @ Wed, 08 Dec 2021 18:20:50: 2000000 INFO @ Wed, 08 Dec 2021 18:20:51: 6000000 INFO @ Wed, 08 Dec 2021 18:20:53: 12000000 INFO @ Wed, 08 Dec 2021 18:20:58: 3000000 INFO @ Wed, 08 Dec 2021 18:20:59: 7000000 INFO @ Wed, 08 Dec 2021 18:20:59: 13000000 INFO @ Wed, 08 Dec 2021 18:21:06: 4000000 INFO @ Wed, 08 Dec 2021 18:21:06: 14000000 INFO @ Wed, 08 Dec 2021 18:21:07: 8000000 INFO @ Wed, 08 Dec 2021 18:21:13: 15000000 INFO @ Wed, 08 Dec 2021 18:21:14: 5000000 INFO @ Wed, 08 Dec 2021 18:21:14: 9000000 INFO @ Wed, 08 Dec 2021 18:21:20: 16000000 INFO @ Wed, 08 Dec 2021 18:21:21: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:21:21: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:21:21: #1 total tags in treatment: 5872612 INFO @ Wed, 08 Dec 2021 18:21:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:21:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:21:21: #1 tags after filtering in treatment: 4470357 INFO @ Wed, 08 Dec 2021 18:21:21: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 18:21:21: #1 finished! INFO @ Wed, 08 Dec 2021 18:21:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:21:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:21:22: #2 number of paired peaks: 1026 INFO @ Wed, 08 Dec 2021 18:21:22: start model_add_line... INFO @ Wed, 08 Dec 2021 18:21:22: start X-correlation... INFO @ Wed, 08 Dec 2021 18:21:22: end of X-cor INFO @ Wed, 08 Dec 2021 18:21:22: #2 finished! INFO @ Wed, 08 Dec 2021 18:21:22: #2 predicted fragment length is 273 bps INFO @ Wed, 08 Dec 2021 18:21:22: #2 alternative fragment length(s) may be 273 bps INFO @ Wed, 08 Dec 2021 18:21:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.05_model.r WARNING @ Wed, 08 Dec 2021 18:21:22: #2 Since the d (273) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:21:22: #2 You may need to consider one of the other alternative d(s): 273 WARNING @ Wed, 08 Dec 2021 18:21:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:21:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:21:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:21:22: 6000000 INFO @ Wed, 08 Dec 2021 18:21:22: 10000000 INFO @ Wed, 08 Dec 2021 18:21:30: 7000000 INFO @ Wed, 08 Dec 2021 18:21:30: 11000000 INFO @ Wed, 08 Dec 2021 18:21:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:21:38: 8000000 INFO @ Wed, 08 Dec 2021 18:21:38: 12000000 INFO @ Wed, 08 Dec 2021 18:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.05_summits.bed INFO @ Wed, 08 Dec 2021 18:21:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:21:46: 9000000 INFO @ Wed, 08 Dec 2021 18:21:46: 13000000 INFO @ Wed, 08 Dec 2021 18:21:54: 10000000 INFO @ Wed, 08 Dec 2021 18:21:54: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:22:02: 11000000 INFO @ Wed, 08 Dec 2021 18:22:02: 15000000 INFO @ Wed, 08 Dec 2021 18:22:10: 16000000 INFO @ Wed, 08 Dec 2021 18:22:10: 12000000 INFO @ Wed, 08 Dec 2021 18:22:11: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:22:11: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:22:11: #1 total tags in treatment: 5872612 INFO @ Wed, 08 Dec 2021 18:22:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:22:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:22:11: #1 tags after filtering in treatment: 4470357 INFO @ Wed, 08 Dec 2021 18:22:11: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 18:22:11: #1 finished! INFO @ Wed, 08 Dec 2021 18:22:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:22:11: #2 number of paired peaks: 1026 INFO @ Wed, 08 Dec 2021 18:22:11: start model_add_line... INFO @ Wed, 08 Dec 2021 18:22:11: start X-correlation... INFO @ Wed, 08 Dec 2021 18:22:11: end of X-cor INFO @ Wed, 08 Dec 2021 18:22:11: #2 finished! INFO @ Wed, 08 Dec 2021 18:22:11: #2 predicted fragment length is 273 bps INFO @ Wed, 08 Dec 2021 18:22:11: #2 alternative fragment length(s) may be 273 bps INFO @ Wed, 08 Dec 2021 18:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.10_model.r WARNING @ Wed, 08 Dec 2021 18:22:11: #2 Since the d (273) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:22:11: #2 You may need to consider one of the other alternative d(s): 273 WARNING @ Wed, 08 Dec 2021 18:22:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:22:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:22:17: 13000000 INFO @ Wed, 08 Dec 2021 18:22:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:22:25: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:22:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:22:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:22:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.10_summits.bed INFO @ Wed, 08 Dec 2021 18:22:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (754 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:22:33: 15000000 INFO @ Wed, 08 Dec 2021 18:22:40: 16000000 INFO @ Wed, 08 Dec 2021 18:22:41: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:22:41: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:22:41: #1 total tags in treatment: 5872612 INFO @ Wed, 08 Dec 2021 18:22:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:22:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:22:42: #1 tags after filtering in treatment: 4470357 INFO @ Wed, 08 Dec 2021 18:22:42: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 18:22:42: #1 finished! INFO @ Wed, 08 Dec 2021 18:22:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:22:42: #2 number of paired peaks: 1026 INFO @ Wed, 08 Dec 2021 18:22:42: start model_add_line... INFO @ Wed, 08 Dec 2021 18:22:42: start X-correlation... INFO @ Wed, 08 Dec 2021 18:22:42: end of X-cor INFO @ Wed, 08 Dec 2021 18:22:42: #2 finished! INFO @ Wed, 08 Dec 2021 18:22:42: #2 predicted fragment length is 273 bps INFO @ Wed, 08 Dec 2021 18:22:42: #2 alternative fragment length(s) may be 273 bps INFO @ Wed, 08 Dec 2021 18:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.20_model.r WARNING @ Wed, 08 Dec 2021 18:22:42: #2 Since the d (273) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:22:42: #2 You may need to consider one of the other alternative d(s): 273 WARNING @ Wed, 08 Dec 2021 18:22:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:22:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:22:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:22:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:22:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641196/SRX10641196.20_summits.bed INFO @ Wed, 08 Dec 2021 18:22:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (493 records, 4 fields): 2 millis CompletedMACS2peakCalling