Job ID = 14158383 SRX = SRX10641178 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21556117 spots for SRR14280100/SRR14280100.sra Written 21556117 spots for SRR14280100/SRR14280100.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158982 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:07 21556117 reads; of these: 21556117 (100.00%) were paired; of these: 15270005 (70.84%) aligned concordantly 0 times 5599638 (25.98%) aligned concordantly exactly 1 time 686474 (3.18%) aligned concordantly >1 times ---- 15270005 pairs aligned concordantly 0 times; of these: 2505659 (16.41%) aligned discordantly 1 time ---- 12764346 pairs aligned 0 times concordantly or discordantly; of these: 25528692 mates make up the pairs; of these: 24435010 (95.72%) aligned 0 times 574533 (2.25%) aligned exactly 1 time 519149 (2.03%) aligned >1 times 43.32% overall alignment rate Time searching: 00:20:08 Overall time: 00:20:08 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 16 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] 1145390 / 8770038 = 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 17:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.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 17:05:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:05:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:05:57: 1000000 INFO @ Wed, 08 Dec 2021 17:06:03: 2000000 INFO @ Wed, 08 Dec 2021 17:06:10: 3000000 INFO @ Wed, 08 Dec 2021 17:06:16: 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 17:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.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 17:06:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:06:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:06:23: 5000000 INFO @ Wed, 08 Dec 2021 17:06:27: 1000000 INFO @ Wed, 08 Dec 2021 17:06:30: 6000000 INFO @ Wed, 08 Dec 2021 17:06:34: 2000000 INFO @ Wed, 08 Dec 2021 17:06:37: 7000000 INFO @ Wed, 08 Dec 2021 17:06:41: 3000000 INFO @ Wed, 08 Dec 2021 17:06:44: 8000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 17:06:48: 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 17:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.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 17:06:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:06:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:06:51: 9000000 INFO @ Wed, 08 Dec 2021 17:06:55: 5000000 INFO @ Wed, 08 Dec 2021 17:06:57: 1000000 INFO @ Wed, 08 Dec 2021 17:06:58: 10000000 INFO @ Wed, 08 Dec 2021 17:07:02: 6000000 INFO @ Wed, 08 Dec 2021 17:07:04: 2000000 INFO @ Wed, 08 Dec 2021 17:07:05: 11000000 INFO @ Wed, 08 Dec 2021 17:07:09: 7000000 INFO @ Wed, 08 Dec 2021 17:07:11: 3000000 INFO @ Wed, 08 Dec 2021 17:07:12: 12000000 INFO @ Wed, 08 Dec 2021 17:07:16: 8000000 INFO @ Wed, 08 Dec 2021 17:07:18: 4000000 INFO @ Wed, 08 Dec 2021 17:07:19: 13000000 INFO @ Wed, 08 Dec 2021 17:07:24: 9000000 INFO @ Wed, 08 Dec 2021 17:07:25: 5000000 INFO @ Wed, 08 Dec 2021 17:07:26: 14000000 INFO @ Wed, 08 Dec 2021 17:07:31: 10000000 INFO @ Wed, 08 Dec 2021 17:07:32: 6000000 INFO @ Wed, 08 Dec 2021 17:07:34: 15000000 INFO @ Wed, 08 Dec 2021 17:07:38: 11000000 INFO @ Wed, 08 Dec 2021 17:07:39: 7000000 INFO @ Wed, 08 Dec 2021 17:07:41: 16000000 INFO @ Wed, 08 Dec 2021 17:07:43: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:07:43: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:07:43: #1 total tags in treatment: 5395328 INFO @ Wed, 08 Dec 2021 17:07:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:07:43: #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 17:07:43: #1 tags after filtering in treatment: 5011422 INFO @ Wed, 08 Dec 2021 17:07:43: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:07:43: #1 finished! INFO @ Wed, 08 Dec 2021 17:07:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:07:44: #2 number of paired peaks: 1957 INFO @ Wed, 08 Dec 2021 17:07:44: start model_add_line... INFO @ Wed, 08 Dec 2021 17:07:44: start X-correlation... INFO @ Wed, 08 Dec 2021 17:07:44: end of X-cor INFO @ Wed, 08 Dec 2021 17:07:44: #2 finished! INFO @ Wed, 08 Dec 2021 17:07:44: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 17:07:44: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 17:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.05_model.r WARNING @ Wed, 08 Dec 2021 17:07:44: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:07:44: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 17:07:44: #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 17:07:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:07:45: 12000000 INFO @ Wed, 08 Dec 2021 17:07:46: 8000000 INFO @ Wed, 08 Dec 2021 17:07:52: 13000000 INFO @ Wed, 08 Dec 2021 17:07:53: 9000000 INFO @ Wed, 08 Dec 2021 17:07:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:07:58: 14000000 INFO @ Wed, 08 Dec 2021 17:08:00: 10000000 INFO @ Wed, 08 Dec 2021 17:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.05_summits.bed INFO @ Wed, 08 Dec 2021 17:08:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2462 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:08:05: 15000000 INFO @ Wed, 08 Dec 2021 17:08:07: 11000000 INFO @ Wed, 08 Dec 2021 17:08:12: 16000000 INFO @ Wed, 08 Dec 2021 17:08:14: 12000000 INFO @ Wed, 08 Dec 2021 17:08:15: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:08:15: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:08:15: #1 total tags in treatment: 5395328 INFO @ Wed, 08 Dec 2021 17:08:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:08:15: #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 17:08:15: #1 tags after filtering in treatment: 5011422 INFO @ Wed, 08 Dec 2021 17:08:15: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:08:15: #1 finished! INFO @ Wed, 08 Dec 2021 17:08:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:08:16: #2 number of paired peaks: 1957 INFO @ Wed, 08 Dec 2021 17:08:16: start model_add_line... INFO @ Wed, 08 Dec 2021 17:08:16: start X-correlation... INFO @ Wed, 08 Dec 2021 17:08:16: end of X-cor INFO @ Wed, 08 Dec 2021 17:08:16: #2 finished! INFO @ Wed, 08 Dec 2021 17:08:16: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 17:08:16: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 17:08:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.10_model.r WARNING @ Wed, 08 Dec 2021 17:08:16: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:08:16: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 17:08:16: #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 17:08:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:08:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:08:21: 13000000 INFO @ Wed, 08 Dec 2021 17:08:28: 14000000 INFO @ Wed, 08 Dec 2021 17:08:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:08:35: 15000000 INFO @ Wed, 08 Dec 2021 17:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:08:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:08:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.10_summits.bed INFO @ Wed, 08 Dec 2021 17:08:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:08:41: 16000000 INFO @ Wed, 08 Dec 2021 17:08:44: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:08:44: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:08:44: #1 total tags in treatment: 5395328 INFO @ Wed, 08 Dec 2021 17:08:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:08:44: #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 17:08:44: #1 tags after filtering in treatment: 5011422 INFO @ Wed, 08 Dec 2021 17:08:44: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:08:44: #1 finished! INFO @ Wed, 08 Dec 2021 17:08:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:08:45: #2 number of paired peaks: 1957 INFO @ Wed, 08 Dec 2021 17:08:45: start model_add_line... INFO @ Wed, 08 Dec 2021 17:08:45: start X-correlation... INFO @ Wed, 08 Dec 2021 17:08:45: end of X-cor INFO @ Wed, 08 Dec 2021 17:08:45: #2 finished! INFO @ Wed, 08 Dec 2021 17:08:45: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 17:08:45: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 17:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.20_model.r WARNING @ Wed, 08 Dec 2021 17:08:45: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:08:45: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 17:08:45: #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 17:08:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:08:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:08:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:09:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:09:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:09:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641178/SRX10641178.20_summits.bed INFO @ Wed, 08 Dec 2021 17:09:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 1 millis CompletedMACS2peakCalling