Job ID = 14158978 SRX = SRX8976719 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12602747 spots for SRR12483323/SRR12483323.sra Written 12602747 spots for SRR12483323/SRR12483323.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159287 ("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: 00:10:40 12602747 reads; of these: 12602747 (100.00%) were paired; of these: 899526 (7.14%) aligned concordantly 0 times 9746164 (77.33%) aligned concordantly exactly 1 time 1957057 (15.53%) aligned concordantly >1 times ---- 899526 pairs aligned concordantly 0 times; of these: 511603 (56.87%) aligned discordantly 1 time ---- 387923 pairs aligned 0 times concordantly or discordantly; of these: 775846 mates make up the pairs; of these: 470431 (60.63%) aligned 0 times 125213 (16.14%) aligned exactly 1 time 180202 (23.23%) aligned >1 times 98.13% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 5540394 / 12210635 = 0.4537 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 18:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.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 18:44:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:44:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:45:03: 1000000 INFO @ Wed, 08 Dec 2021 18:45:08: 2000000 INFO @ Wed, 08 Dec 2021 18:45:12: 3000000 INFO @ Wed, 08 Dec 2021 18:45:17: 4000000 INFO @ Wed, 08 Dec 2021 18:45:21: 5000000 INFO @ Wed, 08 Dec 2021 18:45:26: 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 18:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.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 18:45:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:45:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:45:31: 7000000 INFO @ Wed, 08 Dec 2021 18:45:34: 1000000 INFO @ Wed, 08 Dec 2021 18:45:36: 8000000 INFO @ Wed, 08 Dec 2021 18:45:39: 2000000 INFO @ Wed, 08 Dec 2021 18:45:41: 9000000 INFO @ Wed, 08 Dec 2021 18:45:44: 3000000 INFO @ Wed, 08 Dec 2021 18:45:46: 10000000 INFO @ Wed, 08 Dec 2021 18:45:50: 4000000 INFO @ Wed, 08 Dec 2021 18:45:52: 11000000 INFO @ Wed, 08 Dec 2021 18:45:55: 5000000 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 18:45:57: 12000000 INFO @ Wed, 08 Dec 2021 18:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.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 18:45:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:45:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:46:00: 6000000 INFO @ Wed, 08 Dec 2021 18:46:02: 13000000 INFO @ Wed, 08 Dec 2021 18:46:04: 1000000 INFO @ Wed, 08 Dec 2021 18:46:06: 7000000 INFO @ Wed, 08 Dec 2021 18:46:06: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:46:06: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:46:06: #1 total tags in treatment: 6332363 INFO @ Wed, 08 Dec 2021 18:46:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:46:06: #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 18:46:06: #1 tags after filtering in treatment: 5914757 INFO @ Wed, 08 Dec 2021 18:46:06: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:46:06: #1 finished! INFO @ Wed, 08 Dec 2021 18:46:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:46:06: #2 number of paired peaks: 772 WARNING @ Wed, 08 Dec 2021 18:46:06: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Wed, 08 Dec 2021 18:46:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:46:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:46:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:46:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:46:06: #2 predicted fragment length is 168 bps INFO @ Wed, 08 Dec 2021 18:46:06: #2 alternative fragment length(s) may be 4,168 bps INFO @ Wed, 08 Dec 2021 18:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.05_model.r INFO @ Wed, 08 Dec 2021 18:46:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:46:10: 2000000 INFO @ Wed, 08 Dec 2021 18:46:11: 8000000 INFO @ Wed, 08 Dec 2021 18:46:15: 3000000 INFO @ Wed, 08 Dec 2021 18:46:16: 9000000 INFO @ Wed, 08 Dec 2021 18:46:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:46:20: 4000000 INFO @ Wed, 08 Dec 2021 18:46:21: 10000000 INFO @ Wed, 08 Dec 2021 18:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.05_summits.bed INFO @ Wed, 08 Dec 2021 18:46:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (561 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:46:26: 5000000 INFO @ Wed, 08 Dec 2021 18:46:27: 11000000 INFO @ Wed, 08 Dec 2021 18:46:31: 6000000 INFO @ Wed, 08 Dec 2021 18:46:32: 12000000 INFO @ Wed, 08 Dec 2021 18:46:36: 7000000 INFO @ Wed, 08 Dec 2021 18:46:37: 13000000 INFO @ Wed, 08 Dec 2021 18:46:40: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:46:40: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:46:40: #1 total tags in treatment: 6332363 INFO @ Wed, 08 Dec 2021 18:46:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:46:40: #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 18:46:41: #1 tags after filtering in treatment: 5914757 INFO @ Wed, 08 Dec 2021 18:46:41: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:46:41: #1 finished! INFO @ Wed, 08 Dec 2021 18:46:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:46:41: #2 number of paired peaks: 772 WARNING @ Wed, 08 Dec 2021 18:46:41: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Wed, 08 Dec 2021 18:46:41: start model_add_line... INFO @ Wed, 08 Dec 2021 18:46:41: start X-correlation... INFO @ Wed, 08 Dec 2021 18:46:41: end of X-cor INFO @ Wed, 08 Dec 2021 18:46:41: #2 finished! INFO @ Wed, 08 Dec 2021 18:46:41: #2 predicted fragment length is 168 bps INFO @ Wed, 08 Dec 2021 18:46:41: #2 alternative fragment length(s) may be 4,168 bps INFO @ Wed, 08 Dec 2021 18:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.10_model.r INFO @ Wed, 08 Dec 2021 18:46:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:46:42: 8000000 INFO @ Wed, 08 Dec 2021 18:46:47: 9000000 INFO @ Wed, 08 Dec 2021 18:46:51: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:46:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:46:56: 11000000 INFO @ Wed, 08 Dec 2021 18:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.10_summits.bed INFO @ Wed, 08 Dec 2021 18:47:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 181 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:47:01: 12000000 INFO @ Wed, 08 Dec 2021 18:47:05: 13000000 INFO @ Wed, 08 Dec 2021 18:47:09: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:47:09: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:47:09: #1 total tags in treatment: 6332363 INFO @ Wed, 08 Dec 2021 18:47:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:47:09: #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 18:47:09: #1 tags after filtering in treatment: 5914757 INFO @ Wed, 08 Dec 2021 18:47:09: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:47:09: #1 finished! INFO @ Wed, 08 Dec 2021 18:47:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:47:09: #2 number of paired peaks: 772 WARNING @ Wed, 08 Dec 2021 18:47:09: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Wed, 08 Dec 2021 18:47:09: start model_add_line... INFO @ Wed, 08 Dec 2021 18:47:09: start X-correlation... INFO @ Wed, 08 Dec 2021 18:47:09: end of X-cor INFO @ Wed, 08 Dec 2021 18:47:09: #2 finished! INFO @ Wed, 08 Dec 2021 18:47:09: #2 predicted fragment length is 168 bps INFO @ Wed, 08 Dec 2021 18:47:09: #2 alternative fragment length(s) may be 4,168 bps INFO @ Wed, 08 Dec 2021 18:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.20_model.r INFO @ Wed, 08 Dec 2021 18:47:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:47:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:47:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976719/SRX8976719.20_summits.bed INFO @ Wed, 08 Dec 2021 18:47:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (212 records, 4 fields): 2 millis CompletedMACS2peakCalling