Job ID = 14158984 SRX = SRX10641179 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:01 19701260 reads; of these: 19701260 (100.00%) were paired; of these: 12312608 (62.50%) aligned concordantly 0 times 6678795 (33.90%) aligned concordantly exactly 1 time 709857 (3.60%) aligned concordantly >1 times ---- 12312608 pairs aligned concordantly 0 times; of these: 2075638 (16.86%) aligned discordantly 1 time ---- 10236970 pairs aligned 0 times concordantly or discordantly; of these: 20473940 mates make up the pairs; of these: 19615873 (95.81%) aligned 0 times 477998 (2.33%) aligned exactly 1 time 380069 (1.86%) aligned >1 times 50.22% overall alignment rate Time searching: 00:21:01 Overall time: 00:21:01 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] 1324835 / 9427693 = 0.1405 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 19:03:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.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 19:03:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:03:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:04:03: 1000000 INFO @ Wed, 08 Dec 2021 19:04:10: 2000000 INFO @ Wed, 08 Dec 2021 19:04:18: 3000000 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 19:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.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 19:04:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:04:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:04:26: 4000000 INFO @ Wed, 08 Dec 2021 19:04:36: 5000000 INFO @ Wed, 08 Dec 2021 19:04:37: 1000000 INFO @ Wed, 08 Dec 2021 19:04:46: 6000000 INFO @ Wed, 08 Dec 2021 19:04:49: 2000000 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 19:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.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 19:04:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:04:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:04:57: 7000000 INFO @ Wed, 08 Dec 2021 19:05:00: 3000000 INFO @ Wed, 08 Dec 2021 19:05:07: 8000000 INFO @ Wed, 08 Dec 2021 19:05:07: 1000000 INFO @ Wed, 08 Dec 2021 19:05:13: 4000000 INFO @ Wed, 08 Dec 2021 19:05:18: 9000000 INFO @ Wed, 08 Dec 2021 19:05:20: 2000000 INFO @ Wed, 08 Dec 2021 19:05:25: 5000000 INFO @ Wed, 08 Dec 2021 19:05:28: 10000000 INFO @ Wed, 08 Dec 2021 19:05:32: 3000000 INFO @ Wed, 08 Dec 2021 19:05:37: 6000000 INFO @ Wed, 08 Dec 2021 19:05:38: 11000000 INFO @ Wed, 08 Dec 2021 19:05:44: 4000000 INFO @ Wed, 08 Dec 2021 19:05:48: 7000000 INFO @ Wed, 08 Dec 2021 19:05:49: 12000000 INFO @ Wed, 08 Dec 2021 19:05:57: 5000000 INFO @ Wed, 08 Dec 2021 19:05:59: 13000000 INFO @ Wed, 08 Dec 2021 19:05:59: 8000000 INFO @ Wed, 08 Dec 2021 19:06:09: 6000000 INFO @ Wed, 08 Dec 2021 19:06:09: 14000000 INFO @ Wed, 08 Dec 2021 19:06:11: 9000000 INFO @ Wed, 08 Dec 2021 19:06:20: 15000000 INFO @ Wed, 08 Dec 2021 19:06:21: 7000000 INFO @ Wed, 08 Dec 2021 19:06:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:06:30: 16000000 INFO @ Wed, 08 Dec 2021 19:06:34: 8000000 INFO @ Wed, 08 Dec 2021 19:06:34: 11000000 INFO @ Wed, 08 Dec 2021 19:06:40: 17000000 INFO @ Wed, 08 Dec 2021 19:06:42: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:06:42: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:06:42: #1 total tags in treatment: 6286202 INFO @ Wed, 08 Dec 2021 19:06:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:06:42: #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 19:06:42: #1 tags after filtering in treatment: 5850106 INFO @ Wed, 08 Dec 2021 19:06:42: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:06:42: #1 finished! INFO @ Wed, 08 Dec 2021 19:06:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:06:42: #2 number of paired peaks: 2247 INFO @ Wed, 08 Dec 2021 19:06:42: start model_add_line... INFO @ Wed, 08 Dec 2021 19:06:42: start X-correlation... INFO @ Wed, 08 Dec 2021 19:06:42: end of X-cor INFO @ Wed, 08 Dec 2021 19:06:42: #2 finished! INFO @ Wed, 08 Dec 2021 19:06:42: #2 predicted fragment length is 251 bps INFO @ Wed, 08 Dec 2021 19:06:42: #2 alternative fragment length(s) may be 251 bps INFO @ Wed, 08 Dec 2021 19:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.05_model.r WARNING @ Wed, 08 Dec 2021 19:06:42: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:06:42: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Wed, 08 Dec 2021 19:06:42: #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 19:06:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:06:46: 12000000 INFO @ Wed, 08 Dec 2021 19:06:46: 9000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:06:57: 13000000 INFO @ Wed, 08 Dec 2021 19:06:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:06:58: 10000000 INFO @ Wed, 08 Dec 2021 19:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.05_summits.bed INFO @ Wed, 08 Dec 2021 19:07:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4179 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:07:07: 14000000 INFO @ Wed, 08 Dec 2021 19:07:10: 11000000 INFO @ Wed, 08 Dec 2021 19:07:17: 15000000 INFO @ Wed, 08 Dec 2021 19:07:22: 12000000 INFO @ Wed, 08 Dec 2021 19:07:28: 16000000 INFO @ Wed, 08 Dec 2021 19:07:35: 13000000 INFO @ Wed, 08 Dec 2021 19:07:38: 17000000 INFO @ Wed, 08 Dec 2021 19:07:40: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:07:40: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:07:40: #1 total tags in treatment: 6286202 INFO @ Wed, 08 Dec 2021 19:07:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:07:40: #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 19:07:40: #1 tags after filtering in treatment: 5850106 INFO @ Wed, 08 Dec 2021 19:07:40: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:07:40: #1 finished! INFO @ Wed, 08 Dec 2021 19:07:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:07:40: #2 number of paired peaks: 2247 INFO @ Wed, 08 Dec 2021 19:07:40: start model_add_line... INFO @ Wed, 08 Dec 2021 19:07:40: start X-correlation... INFO @ Wed, 08 Dec 2021 19:07:40: end of X-cor INFO @ Wed, 08 Dec 2021 19:07:40: #2 finished! INFO @ Wed, 08 Dec 2021 19:07:40: #2 predicted fragment length is 251 bps INFO @ Wed, 08 Dec 2021 19:07:40: #2 alternative fragment length(s) may be 251 bps INFO @ Wed, 08 Dec 2021 19:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.10_model.r WARNING @ Wed, 08 Dec 2021 19:07:40: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:07:40: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Wed, 08 Dec 2021 19:07:40: #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 19:07:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:07:46: 14000000 INFO @ Wed, 08 Dec 2021 19:07:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:07:57: 15000000 INFO @ Wed, 08 Dec 2021 19:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.10_summits.bed INFO @ Wed, 08 Dec 2021 19:08:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2001 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:08:08: 16000000 INFO @ Wed, 08 Dec 2021 19:08:19: 17000000 INFO @ Wed, 08 Dec 2021 19:08:21: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:08:21: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:08:21: #1 total tags in treatment: 6286202 INFO @ Wed, 08 Dec 2021 19:08:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:08:21: #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 19:08:21: #1 tags after filtering in treatment: 5850106 INFO @ Wed, 08 Dec 2021 19:08:21: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:08:21: #1 finished! INFO @ Wed, 08 Dec 2021 19:08:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:08:21: #2 number of paired peaks: 2247 INFO @ Wed, 08 Dec 2021 19:08:21: start model_add_line... INFO @ Wed, 08 Dec 2021 19:08:21: start X-correlation... INFO @ Wed, 08 Dec 2021 19:08:21: end of X-cor INFO @ Wed, 08 Dec 2021 19:08:21: #2 finished! INFO @ Wed, 08 Dec 2021 19:08:21: #2 predicted fragment length is 251 bps INFO @ Wed, 08 Dec 2021 19:08:21: #2 alternative fragment length(s) may be 251 bps INFO @ Wed, 08 Dec 2021 19:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.20_model.r WARNING @ Wed, 08 Dec 2021 19:08:21: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:08:21: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Wed, 08 Dec 2021 19:08:21: #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 19:08:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:08:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641179/SRX10641179.20_summits.bed INFO @ Wed, 08 Dec 2021 19:08:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (673 records, 4 fields): 1 millis CompletedMACS2peakCalling