Job ID = 14158018 SRX = SRX10641215 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16498469 spots for SRR14280063/SRR14280063.sra Written 16498469 spots for SRR14280063/SRR14280063.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158298 ("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: 00:18:25 16498469 reads; of these: 16498469 (100.00%) were paired; of these: 11709804 (70.98%) aligned concordantly 0 times 4006242 (24.28%) aligned concordantly exactly 1 time 782423 (4.74%) aligned concordantly >1 times ---- 11709804 pairs aligned concordantly 0 times; of these: 2542274 (21.71%) aligned discordantly 1 time ---- 9167530 pairs aligned 0 times concordantly or discordantly; of these: 18335060 mates make up the pairs; of these: 16987209 (92.65%) aligned 0 times 773825 (4.22%) aligned exactly 1 time 574026 (3.13%) aligned >1 times 48.52% overall alignment rate Time searching: 00:18:25 Overall time: 00:18:25 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] 954739 / 7309210 = 0.1306 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 14:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.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 14:21:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:21:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:21:37: 1000000 INFO @ Wed, 08 Dec 2021 14:21:43: 2000000 INFO @ Wed, 08 Dec 2021 14:21:49: 3000000 INFO @ Wed, 08 Dec 2021 14:21:55: 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 14:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.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 14:22:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:01: 5000000 INFO @ Wed, 08 Dec 2021 14:22:07: 1000000 INFO @ Wed, 08 Dec 2021 14:22:07: 6000000 INFO @ Wed, 08 Dec 2021 14:22:13: 7000000 INFO @ Wed, 08 Dec 2021 14:22:13: 2000000 INFO @ Wed, 08 Dec 2021 14:22:19: 8000000 INFO @ Wed, 08 Dec 2021 14:22:19: 3000000 INFO @ Wed, 08 Dec 2021 14:22:25: 9000000 INFO @ Wed, 08 Dec 2021 14:22:25: 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 @ Wed, 08 Dec 2021 14:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.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 14:22:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:31: 10000000 INFO @ Wed, 08 Dec 2021 14:22:31: 5000000 INFO @ Wed, 08 Dec 2021 14:22:37: 1000000 INFO @ Wed, 08 Dec 2021 14:22:38: 11000000 INFO @ Wed, 08 Dec 2021 14:22:38: 6000000 INFO @ Wed, 08 Dec 2021 14:22:43: 2000000 INFO @ Wed, 08 Dec 2021 14:22:44: 7000000 INFO @ Wed, 08 Dec 2021 14:22:44: 12000000 INFO @ Wed, 08 Dec 2021 14:22:49: 3000000 INFO @ Wed, 08 Dec 2021 14:22:50: 8000000 INFO @ Wed, 08 Dec 2021 14:22:50: 13000000 INFO @ Wed, 08 Dec 2021 14:22:56: 4000000 INFO @ Wed, 08 Dec 2021 14:22:56: 9000000 INFO @ Wed, 08 Dec 2021 14:22:56: 14000000 INFO @ Wed, 08 Dec 2021 14:22:57: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:22:57: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:22:57: #1 total tags in treatment: 4098863 INFO @ Wed, 08 Dec 2021 14:22:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:22:57: #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 14:22:57: #1 tags after filtering in treatment: 3786432 INFO @ Wed, 08 Dec 2021 14:22:57: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:22:57: #1 finished! INFO @ Wed, 08 Dec 2021 14:22:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:22:57: #2 number of paired peaks: 559 WARNING @ Wed, 08 Dec 2021 14:22:57: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Wed, 08 Dec 2021 14:22:57: start model_add_line... INFO @ Wed, 08 Dec 2021 14:22:57: start X-correlation... INFO @ Wed, 08 Dec 2021 14:22:57: end of X-cor INFO @ Wed, 08 Dec 2021 14:22:57: #2 finished! INFO @ Wed, 08 Dec 2021 14:22:57: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 14:22:57: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 14:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.05_model.r WARNING @ Wed, 08 Dec 2021 14:22:57: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:22:57: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 14:22:57: #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 14:22:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:23:02: 5000000 INFO @ Wed, 08 Dec 2021 14:23:02: 10000000 INFO @ Wed, 08 Dec 2021 14:23:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:23:08: 6000000 INFO @ Wed, 08 Dec 2021 14:23:08: 11000000 INFO @ Wed, 08 Dec 2021 14:23:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:23:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:23:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.05_summits.bed INFO @ Wed, 08 Dec 2021 14:23:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:23:14: 7000000 INFO @ Wed, 08 Dec 2021 14:23:14: 12000000 INFO @ Wed, 08 Dec 2021 14:23:20: 8000000 INFO @ Wed, 08 Dec 2021 14:23:20: 13000000 INFO @ Wed, 08 Dec 2021 14:23:26: 9000000 INFO @ Wed, 08 Dec 2021 14:23:27: 14000000 INFO @ Wed, 08 Dec 2021 14:23:27: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:23:27: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:23:27: #1 total tags in treatment: 4098863 INFO @ Wed, 08 Dec 2021 14:23:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:23:27: #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 14:23:27: #1 tags after filtering in treatment: 3786432 INFO @ Wed, 08 Dec 2021 14:23:27: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:23:27: #1 finished! INFO @ Wed, 08 Dec 2021 14:23:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:23:28: #2 number of paired peaks: 559 WARNING @ Wed, 08 Dec 2021 14:23:28: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Wed, 08 Dec 2021 14:23:28: start model_add_line... INFO @ Wed, 08 Dec 2021 14:23:28: start X-correlation... INFO @ Wed, 08 Dec 2021 14:23:28: end of X-cor INFO @ Wed, 08 Dec 2021 14:23:28: #2 finished! INFO @ Wed, 08 Dec 2021 14:23:28: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 14:23:28: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 14:23:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.10_model.r WARNING @ Wed, 08 Dec 2021 14:23:28: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:23:28: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 14:23:28: #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 14:23:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:23:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:23:33: 10000000 INFO @ Wed, 08 Dec 2021 14:23:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:23:39: 11000000 INFO @ Wed, 08 Dec 2021 14:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:23:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.10_summits.bed INFO @ Wed, 08 Dec 2021 14:23:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:23:45: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:23:51: 13000000 INFO @ Wed, 08 Dec 2021 14:23:57: 14000000 INFO @ Wed, 08 Dec 2021 14:23:58: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:23:58: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:23:58: #1 total tags in treatment: 4098863 INFO @ Wed, 08 Dec 2021 14:23:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:23:58: #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 14:23:58: #1 tags after filtering in treatment: 3786432 INFO @ Wed, 08 Dec 2021 14:23:58: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:23:58: #1 finished! INFO @ Wed, 08 Dec 2021 14:23:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:23:58: #2 number of paired peaks: 559 WARNING @ Wed, 08 Dec 2021 14:23:58: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Wed, 08 Dec 2021 14:23:58: start model_add_line... INFO @ Wed, 08 Dec 2021 14:23:58: start X-correlation... INFO @ Wed, 08 Dec 2021 14:23:58: end of X-cor INFO @ Wed, 08 Dec 2021 14:23:58: #2 finished! INFO @ Wed, 08 Dec 2021 14:23:58: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 14:23:58: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 14:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.20_model.r WARNING @ Wed, 08 Dec 2021 14:23:58: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:23:58: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 14:23:58: #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 14:23:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:24:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641215/SRX10641215.20_summits.bed INFO @ Wed, 08 Dec 2021 14:24:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。