Job ID = 12264749 SRX = SRX2333002 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 43457363 spots for SRR5000682/SRR5000682.sra Written 43457363 spots for SRR5000682/SRR5000682.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265498 ("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: 00:28:19 43457363 reads; of these: 43457363 (100.00%) were paired; of these: 35435884 (81.54%) aligned concordantly 0 times 6652092 (15.31%) aligned concordantly exactly 1 time 1369387 (3.15%) aligned concordantly >1 times ---- 35435884 pairs aligned concordantly 0 times; of these: 2262460 (6.38%) aligned discordantly 1 time ---- 33173424 pairs aligned 0 times concordantly or discordantly; of these: 66346848 mates make up the pairs; of these: 65245783 (98.34%) aligned 0 times 422936 (0.64%) aligned exactly 1 time 678129 (1.02%) aligned >1 times 24.93% overall alignment rate Time searching: 00:28:19 Overall time: 00:28:19 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] 1589474 / 10228955 = 0.1554 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.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 @ Sat, 03 Apr 2021 07:00:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:00:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:00:42: 1000000 INFO @ Sat, 03 Apr 2021 07:00:51: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:01:00: 3000000 INFO @ Sat, 03 Apr 2021 07:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.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 @ Sat, 03 Apr 2021 07:01:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:01:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:01:08: 4000000 INFO @ Sat, 03 Apr 2021 07:01:11: 1000000 INFO @ Sat, 03 Apr 2021 07:01:18: 5000000 INFO @ Sat, 03 Apr 2021 07:01:20: 2000000 INFO @ Sat, 03 Apr 2021 07:01:27: 6000000 INFO @ Sat, 03 Apr 2021 07:01:28: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.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 @ Sat, 03 Apr 2021 07:01:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:01:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:01:36: 7000000 INFO @ Sat, 03 Apr 2021 07:01:38: 4000000 INFO @ Sat, 03 Apr 2021 07:01:42: 1000000 INFO @ Sat, 03 Apr 2021 07:01:45: 8000000 INFO @ Sat, 03 Apr 2021 07:01:49: 5000000 INFO @ Sat, 03 Apr 2021 07:01:55: 2000000 INFO @ Sat, 03 Apr 2021 07:01:55: 9000000 INFO @ Sat, 03 Apr 2021 07:01:59: 6000000 INFO @ Sat, 03 Apr 2021 07:02:04: 3000000 INFO @ Sat, 03 Apr 2021 07:02:04: 10000000 INFO @ Sat, 03 Apr 2021 07:02:09: 7000000 INFO @ Sat, 03 Apr 2021 07:02:12: 4000000 INFO @ Sat, 03 Apr 2021 07:02:13: 11000000 INFO @ Sat, 03 Apr 2021 07:02:18: 8000000 INFO @ Sat, 03 Apr 2021 07:02:20: 5000000 INFO @ Sat, 03 Apr 2021 07:02:22: 12000000 INFO @ Sat, 03 Apr 2021 07:02:27: 9000000 INFO @ Sat, 03 Apr 2021 07:02:29: 6000000 INFO @ Sat, 03 Apr 2021 07:02:30: 13000000 INFO @ Sat, 03 Apr 2021 07:02:36: 10000000 INFO @ Sat, 03 Apr 2021 07:02:38: 7000000 INFO @ Sat, 03 Apr 2021 07:02:39: 14000000 INFO @ Sat, 03 Apr 2021 07:02:44: 11000000 INFO @ Sat, 03 Apr 2021 07:02:46: 8000000 INFO @ Sat, 03 Apr 2021 07:02:47: 15000000 INFO @ Sat, 03 Apr 2021 07:02:53: 12000000 INFO @ Sat, 03 Apr 2021 07:02:54: 9000000 INFO @ Sat, 03 Apr 2021 07:02:56: 16000000 INFO @ Sat, 03 Apr 2021 07:03:01: 13000000 INFO @ Sat, 03 Apr 2021 07:03:03: 10000000 INFO @ Sat, 03 Apr 2021 07:03:04: 17000000 INFO @ Sat, 03 Apr 2021 07:03:10: 14000000 INFO @ Sat, 03 Apr 2021 07:03:11: 11000000 INFO @ Sat, 03 Apr 2021 07:03:13: 18000000 INFO @ Sat, 03 Apr 2021 07:03:17: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:03:17: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:03:17: #1 total tags in treatment: 6635688 INFO @ Sat, 03 Apr 2021 07:03:17: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:03:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:03:17: #1 tags after filtering in treatment: 4997838 INFO @ Sat, 03 Apr 2021 07:03:17: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:03:17: #1 finished! INFO @ Sat, 03 Apr 2021 07:03:17: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:03:18: 15000000 INFO @ Sat, 03 Apr 2021 07:03:18: #2 number of paired peaks: 508 WARNING @ Sat, 03 Apr 2021 07:03:18: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Sat, 03 Apr 2021 07:03:18: start model_add_line... INFO @ Sat, 03 Apr 2021 07:03:18: start X-correlation... INFO @ Sat, 03 Apr 2021 07:03:18: end of X-cor INFO @ Sat, 03 Apr 2021 07:03:18: #2 finished! INFO @ Sat, 03 Apr 2021 07:03:18: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 07:03:18: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 03 Apr 2021 07:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.05_model.r WARNING @ Sat, 03 Apr 2021 07:03:18: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:03:18: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 03 Apr 2021 07:03:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:03:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:03:19: 12000000 INFO @ Sat, 03 Apr 2021 07:03:26: 16000000 INFO @ Sat, 03 Apr 2021 07:03:27: 13000000 INFO @ Sat, 03 Apr 2021 07:03:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:03:34: 17000000 INFO @ Sat, 03 Apr 2021 07:03:35: 14000000 INFO @ Sat, 03 Apr 2021 07:03:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:03:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:03:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.05_summits.bed INFO @ Sat, 03 Apr 2021 07:03:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2874 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:03:42: 18000000 INFO @ Sat, 03 Apr 2021 07:03:43: 15000000 INFO @ Sat, 03 Apr 2021 07:03:46: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:03:46: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:03:46: #1 total tags in treatment: 6635688 INFO @ Sat, 03 Apr 2021 07:03:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:03:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:03:46: #1 tags after filtering in treatment: 4997838 INFO @ Sat, 03 Apr 2021 07:03:46: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:03:46: #1 finished! INFO @ Sat, 03 Apr 2021 07:03:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:03:47: #2 number of paired peaks: 508 WARNING @ Sat, 03 Apr 2021 07:03:47: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Sat, 03 Apr 2021 07:03:47: start model_add_line... INFO @ Sat, 03 Apr 2021 07:03:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:03:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:03:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:03:47: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 07:03:47: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 03 Apr 2021 07:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.10_model.r WARNING @ Sat, 03 Apr 2021 07:03:47: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:03:47: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 03 Apr 2021 07:03:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:03:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:03:51: 16000000 INFO @ Sat, 03 Apr 2021 07:03:58: 17000000 INFO @ Sat, 03 Apr 2021 07:03:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:04:06: 18000000 INFO @ Sat, 03 Apr 2021 07:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.10_summits.bed INFO @ Sat, 03 Apr 2021 07:04:06: Done! pass1 - making usageList (7 chroms): 13 millis pass2 - checking and writing primary data (1198 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:04:09: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:04:09: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:04:09: #1 total tags in treatment: 6635688 INFO @ Sat, 03 Apr 2021 07:04:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:04:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:04:09: #1 tags after filtering in treatment: 4997838 INFO @ Sat, 03 Apr 2021 07:04:09: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:04:09: #1 finished! INFO @ Sat, 03 Apr 2021 07:04:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:04:10: #2 number of paired peaks: 508 WARNING @ Sat, 03 Apr 2021 07:04:10: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Sat, 03 Apr 2021 07:04:10: start model_add_line... INFO @ Sat, 03 Apr 2021 07:04:10: start X-correlation... INFO @ Sat, 03 Apr 2021 07:04:10: end of X-cor INFO @ Sat, 03 Apr 2021 07:04:10: #2 finished! INFO @ Sat, 03 Apr 2021 07:04:10: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 07:04:10: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 03 Apr 2021 07:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.20_model.r WARNING @ Sat, 03 Apr 2021 07:04:10: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:04:10: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 03 Apr 2021 07:04:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:04:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:04:10: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:04:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333002/SRX2333002.20_summits.bed INFO @ Sat, 03 Apr 2021 07:04:27: Done! pass1 - making usageList (6 chroms): 8 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。