Job ID = 14158989 SRX = SRX8976720 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12492052 spots for SRR12483324/SRR12483324.sra Written 12492052 spots for SRR12483324/SRR12483324.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159291 ("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: 00:10:58 12492052 reads; of these: 12492052 (100.00%) were paired; of these: 896658 (7.18%) aligned concordantly 0 times 9653193 (77.27%) aligned concordantly exactly 1 time 1942201 (15.55%) aligned concordantly >1 times ---- 896658 pairs aligned concordantly 0 times; of these: 511398 (57.03%) aligned discordantly 1 time ---- 385260 pairs aligned 0 times concordantly or discordantly; of these: 770520 mates make up the pairs; of these: 459898 (59.69%) aligned 0 times 128003 (16.61%) aligned exactly 1 time 182619 (23.70%) aligned >1 times 98.16% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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 12 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] 5465092 / 12102317 = 0.4516 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 18:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.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 18:49:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:49:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:49:47: 1000000 INFO @ Wed, 08 Dec 2021 18:49:52: 2000000 INFO @ Wed, 08 Dec 2021 18:49:56: 3000000 INFO @ Wed, 08 Dec 2021 18:50:01: 4000000 INFO @ Wed, 08 Dec 2021 18:50:06: 5000000 INFO @ Wed, 08 Dec 2021 18:50:10: 6000000 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 18:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.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 18:50:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:50:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:50:15: 7000000 INFO @ Wed, 08 Dec 2021 18:50:18: 1000000 INFO @ Wed, 08 Dec 2021 18:50:20: 8000000 INFO @ Wed, 08 Dec 2021 18:50:23: 2000000 INFO @ Wed, 08 Dec 2021 18:50:25: 9000000 INFO @ Wed, 08 Dec 2021 18:50:28: 3000000 INFO @ Wed, 08 Dec 2021 18:50:30: 10000000 INFO @ Wed, 08 Dec 2021 18:50:33: 4000000 INFO @ Wed, 08 Dec 2021 18:50:35: 11000000 INFO @ Wed, 08 Dec 2021 18:50:38: 5000000 INFO @ Wed, 08 Dec 2021 18:50:40: 12000000 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 18:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.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 18:50:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:50:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:50:44: 6000000 INFO @ Wed, 08 Dec 2021 18:50:45: 13000000 INFO @ Wed, 08 Dec 2021 18:50:48: 1000000 INFO @ Wed, 08 Dec 2021 18:50:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:50:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:50:48: #1 total tags in treatment: 6299279 INFO @ Wed, 08 Dec 2021 18:50:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:50:48: #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 18:50:49: #1 tags after filtering in treatment: 5885313 INFO @ Wed, 08 Dec 2021 18:50:49: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:50:49: #1 finished! INFO @ Wed, 08 Dec 2021 18:50:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:50:49: #2 number of paired peaks: 768 WARNING @ Wed, 08 Dec 2021 18:50:49: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Wed, 08 Dec 2021 18:50:49: start model_add_line... INFO @ Wed, 08 Dec 2021 18:50:49: 7000000 INFO @ Wed, 08 Dec 2021 18:50:49: start X-correlation... INFO @ Wed, 08 Dec 2021 18:50:49: end of X-cor INFO @ Wed, 08 Dec 2021 18:50:49: #2 finished! INFO @ Wed, 08 Dec 2021 18:50:49: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:50:49: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.05_model.r INFO @ Wed, 08 Dec 2021 18:50:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:50:54: 2000000 INFO @ Wed, 08 Dec 2021 18:50:54: 8000000 INFO @ Wed, 08 Dec 2021 18:50:59: 3000000 INFO @ Wed, 08 Dec 2021 18:51:00: 9000000 INFO @ Wed, 08 Dec 2021 18:51:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:51:04: 4000000 INFO @ Wed, 08 Dec 2021 18:51:05: 10000000 INFO @ Wed, 08 Dec 2021 18:51:09: 5000000 INFO @ Wed, 08 Dec 2021 18:51:10: 11000000 INFO @ Wed, 08 Dec 2021 18:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:51:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.05_summits.bed INFO @ Wed, 08 Dec 2021 18:51:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (552 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:51:14: 6000000 INFO @ Wed, 08 Dec 2021 18:51:15: 12000000 INFO @ Wed, 08 Dec 2021 18:51:20: 7000000 INFO @ Wed, 08 Dec 2021 18:51:20: 13000000 INFO @ Wed, 08 Dec 2021 18:51:23: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:51:23: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:51:23: #1 total tags in treatment: 6299279 INFO @ Wed, 08 Dec 2021 18:51:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:51:23: #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 18:51:23: #1 tags after filtering in treatment: 5885313 INFO @ Wed, 08 Dec 2021 18:51:23: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:51:23: #1 finished! INFO @ Wed, 08 Dec 2021 18:51:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:51:24: #2 number of paired peaks: 768 WARNING @ Wed, 08 Dec 2021 18:51:24: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Wed, 08 Dec 2021 18:51:24: start model_add_line... INFO @ Wed, 08 Dec 2021 18:51:24: start X-correlation... INFO @ Wed, 08 Dec 2021 18:51:24: end of X-cor INFO @ Wed, 08 Dec 2021 18:51:24: #2 finished! INFO @ Wed, 08 Dec 2021 18:51:24: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:51:24: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.10_model.r INFO @ Wed, 08 Dec 2021 18:51:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:51:25: 8000000 INFO @ Wed, 08 Dec 2021 18:51:29: 9000000 INFO @ Wed, 08 Dec 2021 18:51:34: 10000000 INFO @ Wed, 08 Dec 2021 18:51:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:51:38: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.10_summits.bed INFO @ Wed, 08 Dec 2021 18:51:43: Done! INFO @ Wed, 08 Dec 2021 18:51:43: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (332 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:51:48: 13000000 INFO @ Wed, 08 Dec 2021 18:51:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:51:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:51:51: #1 total tags in treatment: 6299279 INFO @ Wed, 08 Dec 2021 18:51:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:51:51: #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 18:51:51: #1 tags after filtering in treatment: 5885313 INFO @ Wed, 08 Dec 2021 18:51:51: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:51:51: #1 finished! INFO @ Wed, 08 Dec 2021 18:51:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:51:51: #2 number of paired peaks: 768 WARNING @ Wed, 08 Dec 2021 18:51:51: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Wed, 08 Dec 2021 18:51:51: start model_add_line... INFO @ Wed, 08 Dec 2021 18:51:51: start X-correlation... INFO @ Wed, 08 Dec 2021 18:51:51: end of X-cor INFO @ Wed, 08 Dec 2021 18:51:51: #2 finished! INFO @ Wed, 08 Dec 2021 18:51:51: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:51:51: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.20_model.r INFO @ Wed, 08 Dec 2021 18:51:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:52:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976720/SRX8976720.20_summits.bed INFO @ Wed, 08 Dec 2021 18:52:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 2 millis CompletedMACS2peakCalling