Job ID = 14160340 SRX = SRX9567169 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22845636 spots for SRR13125144/SRR13125144.sra Written 22845636 spots for SRR13125144/SRR13125144.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160603 ("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: 01:09:07 22845636 reads; of these: 22845636 (100.00%) were paired; of these: 9375593 (41.04%) aligned concordantly 0 times 7883514 (34.51%) aligned concordantly exactly 1 time 5586529 (24.45%) aligned concordantly >1 times ---- 9375593 pairs aligned concordantly 0 times; of these: 6320533 (67.41%) aligned discordantly 1 time ---- 3055060 pairs aligned 0 times concordantly or discordantly; of these: 6110120 mates make up the pairs; of these: 2908008 (47.59%) aligned 0 times 1463638 (23.95%) aligned exactly 1 time 1738474 (28.45%) aligned >1 times 93.64% overall alignment rate Time searching: 01:09:07 Overall time: 01:09:07 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 32 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] 15408287 / 19767820 = 0.7795 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 @ Thu, 09 Dec 2021 02:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.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 @ Thu, 09 Dec 2021 02:55:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:55:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:55:45: 1000000 INFO @ Thu, 09 Dec 2021 02:55:51: 2000000 INFO @ Thu, 09 Dec 2021 02:55:57: 3000000 INFO @ Thu, 09 Dec 2021 02:56:04: 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 @ Thu, 09 Dec 2021 02:56:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.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 @ Thu, 09 Dec 2021 02:56:08: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:56:08: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:56:10: 5000000 INFO @ Thu, 09 Dec 2021 02:56:16: 1000000 INFO @ Thu, 09 Dec 2021 02:56:17: 6000000 INFO @ Thu, 09 Dec 2021 02:56:23: 2000000 INFO @ Thu, 09 Dec 2021 02:56:24: 7000000 INFO @ Thu, 09 Dec 2021 02:56:30: 3000000 INFO @ Thu, 09 Dec 2021 02:56:31: 8000000 INFO @ Thu, 09 Dec 2021 02:56:36: 4000000 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 @ Thu, 09 Dec 2021 02:56:38: 9000000 INFO @ Thu, 09 Dec 2021 02:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.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 @ Thu, 09 Dec 2021 02:56:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:56:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:56:43: 5000000 INFO @ Thu, 09 Dec 2021 02:56:45: 10000000 INFO @ Thu, 09 Dec 2021 02:56:45: 1000000 INFO @ Thu, 09 Dec 2021 02:56:50: 6000000 INFO @ Thu, 09 Dec 2021 02:56:52: 11000000 INFO @ Thu, 09 Dec 2021 02:56:53: 2000000 INFO @ Thu, 09 Dec 2021 02:56:57: 7000000 INFO @ Thu, 09 Dec 2021 02:56:59: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:56:59: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:56:59: #1 total tags in treatment: 3069184 INFO @ Thu, 09 Dec 2021 02:56:59: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:56:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:56:59: #1 tags after filtering in treatment: 2043888 INFO @ Thu, 09 Dec 2021 02:56:59: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 09 Dec 2021 02:56:59: #1 finished! INFO @ Thu, 09 Dec 2021 02:56:59: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:56:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:56:59: #2 number of paired peaks: 1181 INFO @ Thu, 09 Dec 2021 02:56:59: start model_add_line... INFO @ Thu, 09 Dec 2021 02:56:59: start X-correlation... INFO @ Thu, 09 Dec 2021 02:56:59: end of X-cor INFO @ Thu, 09 Dec 2021 02:56:59: #2 finished! INFO @ Thu, 09 Dec 2021 02:56:59: #2 predicted fragment length is 292 bps INFO @ Thu, 09 Dec 2021 02:56:59: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 09 Dec 2021 02:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.05_model.r WARNING @ Thu, 09 Dec 2021 02:56:59: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:56:59: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Thu, 09 Dec 2021 02:56:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:56:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:57:00: 3000000 INFO @ Thu, 09 Dec 2021 02:57:04: 8000000 INFO @ Thu, 09 Dec 2021 02:57:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:57:07: 4000000 INFO @ Thu, 09 Dec 2021 02:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.05_summits.bed INFO @ Thu, 09 Dec 2021 02:57:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (939 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:57:11: 9000000 INFO @ Thu, 09 Dec 2021 02:57:13: 5000000 INFO @ Thu, 09 Dec 2021 02:57:18: 10000000 INFO @ Thu, 09 Dec 2021 02:57:20: 6000000 INFO @ Thu, 09 Dec 2021 02:57:25: 11000000 INFO @ Thu, 09 Dec 2021 02:57:27: 7000000 INFO @ Thu, 09 Dec 2021 02:57:32: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:57:32: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:57:32: #1 total tags in treatment: 3069184 INFO @ Thu, 09 Dec 2021 02:57:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:57:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:57:32: #1 tags after filtering in treatment: 2043888 INFO @ Thu, 09 Dec 2021 02:57:32: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 09 Dec 2021 02:57:32: #1 finished! INFO @ Thu, 09 Dec 2021 02:57:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:57:32: #2 number of paired peaks: 1181 INFO @ Thu, 09 Dec 2021 02:57:32: start model_add_line... INFO @ Thu, 09 Dec 2021 02:57:32: start X-correlation... INFO @ Thu, 09 Dec 2021 02:57:32: end of X-cor INFO @ Thu, 09 Dec 2021 02:57:32: #2 finished! INFO @ Thu, 09 Dec 2021 02:57:32: #2 predicted fragment length is 292 bps INFO @ Thu, 09 Dec 2021 02:57:32: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 09 Dec 2021 02:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.10_model.r WARNING @ Thu, 09 Dec 2021 02:57:32: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:57:32: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Thu, 09 Dec 2021 02:57:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:57:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:57:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:57:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:57:38: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.10_summits.bed INFO @ Thu, 09 Dec 2021 02:57:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:57:41: 9000000 INFO @ Thu, 09 Dec 2021 02:57:48: 10000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:57:54: 11000000 INFO @ Thu, 09 Dec 2021 02:58:00: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:58:00: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:58:00: #1 total tags in treatment: 3069184 INFO @ Thu, 09 Dec 2021 02:58:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:58:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:58:00: #1 tags after filtering in treatment: 2043888 INFO @ Thu, 09 Dec 2021 02:58:00: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 09 Dec 2021 02:58:00: #1 finished! INFO @ Thu, 09 Dec 2021 02:58:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:58:00: #2 number of paired peaks: 1181 INFO @ Thu, 09 Dec 2021 02:58:00: start model_add_line... INFO @ Thu, 09 Dec 2021 02:58:00: start X-correlation... INFO @ Thu, 09 Dec 2021 02:58:01: end of X-cor INFO @ Thu, 09 Dec 2021 02:58:01: #2 finished! INFO @ Thu, 09 Dec 2021 02:58:01: #2 predicted fragment length is 292 bps INFO @ Thu, 09 Dec 2021 02:58:01: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 09 Dec 2021 02:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.20_model.r WARNING @ Thu, 09 Dec 2021 02:58:01: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:58:01: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Thu, 09 Dec 2021 02:58:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:58:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:58:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567169/SRX9567169.20_summits.bed INFO @ Thu, 09 Dec 2021 02:58:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (478 records, 4 fields): 2 millis CompletedMACS2peakCalling