Job ID = 14158217 SRX = SRX10641202 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: 00:38:52 21797330 reads; of these: 21797330 (100.00%) were paired; of these: 15096650 (69.26%) aligned concordantly 0 times 3628647 (16.65%) aligned concordantly exactly 1 time 3072033 (14.09%) aligned concordantly >1 times ---- 15096650 pairs aligned concordantly 0 times; of these: 1846366 (12.23%) aligned discordantly 1 time ---- 13250284 pairs aligned 0 times concordantly or discordantly; of these: 26500568 mates make up the pairs; of these: 25324731 (95.56%) aligned 0 times 564879 (2.13%) aligned exactly 1 time 610958 (2.31%) aligned >1 times 41.91% overall alignment rate Time searching: 00:38:52 Overall time: 00:38:52 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] 2115888 / 8512691 = 0.2486 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 15:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.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 15:38:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:38:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:38:18: 1000000 INFO @ Wed, 08 Dec 2021 15:38:29: 2000000 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 15:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.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 15:38:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:38:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:38:39: 3000000 INFO @ Wed, 08 Dec 2021 15:38:49: 4000000 INFO @ Wed, 08 Dec 2021 15:38:50: 1000000 INFO @ Wed, 08 Dec 2021 15:39:00: 5000000 INFO @ Wed, 08 Dec 2021 15:39:03: 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 15:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.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 15:39:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:39:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:39:11: 6000000 INFO @ Wed, 08 Dec 2021 15:39:15: 3000000 INFO @ Wed, 08 Dec 2021 15:39:20: 1000000 INFO @ Wed, 08 Dec 2021 15:39:23: 7000000 INFO @ Wed, 08 Dec 2021 15:39:28: 4000000 INFO @ Wed, 08 Dec 2021 15:39:31: 2000000 INFO @ Wed, 08 Dec 2021 15:39:34: 8000000 INFO @ Wed, 08 Dec 2021 15:39:41: 5000000 INFO @ Wed, 08 Dec 2021 15:39:42: 3000000 INFO @ Wed, 08 Dec 2021 15:39:45: 9000000 INFO @ Wed, 08 Dec 2021 15:39:53: 6000000 INFO @ Wed, 08 Dec 2021 15:39:54: 4000000 INFO @ Wed, 08 Dec 2021 15:39:57: 10000000 INFO @ Wed, 08 Dec 2021 15:40:05: 5000000 INFO @ Wed, 08 Dec 2021 15:40:06: 7000000 INFO @ Wed, 08 Dec 2021 15:40:08: 11000000 INFO @ Wed, 08 Dec 2021 15:40:17: 6000000 INFO @ Wed, 08 Dec 2021 15:40:18: 8000000 INFO @ Wed, 08 Dec 2021 15:40:20: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:40:28: 7000000 INFO @ Wed, 08 Dec 2021 15:40:31: 9000000 INFO @ Wed, 08 Dec 2021 15:40:31: 13000000 INFO @ Wed, 08 Dec 2021 15:40:40: 8000000 INFO @ Wed, 08 Dec 2021 15:40:43: 10000000 INFO @ Wed, 08 Dec 2021 15:40:43: 14000000 INFO @ Wed, 08 Dec 2021 15:40:43: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:40:43: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:40:43: #1 total tags in treatment: 4832890 INFO @ Wed, 08 Dec 2021 15:40:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:40:43: #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 15:40:43: #1 tags after filtering in treatment: 3437289 INFO @ Wed, 08 Dec 2021 15:40:43: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 08 Dec 2021 15:40:43: #1 finished! INFO @ Wed, 08 Dec 2021 15:40:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:40:43: #2 number of paired peaks: 1076 INFO @ Wed, 08 Dec 2021 15:40:43: start model_add_line... INFO @ Wed, 08 Dec 2021 15:40:44: start X-correlation... INFO @ Wed, 08 Dec 2021 15:40:44: end of X-cor INFO @ Wed, 08 Dec 2021 15:40:44: #2 finished! INFO @ Wed, 08 Dec 2021 15:40:44: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 15:40:44: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 15:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.05_model.r WARNING @ Wed, 08 Dec 2021 15:40:44: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:40:44: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 15:40:44: #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 15:40:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:40:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:40:51: 9000000 INFO @ Wed, 08 Dec 2021 15:40:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:40:55: 11000000 INFO @ Wed, 08 Dec 2021 15:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.05_summits.bed INFO @ Wed, 08 Dec 2021 15:40:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (829 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:41:02: 10000000 INFO @ Wed, 08 Dec 2021 15:41:07: 12000000 INFO @ Wed, 08 Dec 2021 15:41:13: 11000000 INFO @ Wed, 08 Dec 2021 15:41:19: 13000000 INFO @ Wed, 08 Dec 2021 15:41:24: 12000000 INFO @ Wed, 08 Dec 2021 15:41:31: 14000000 INFO @ Wed, 08 Dec 2021 15:41:31: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:41:31: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:41:31: #1 total tags in treatment: 4832890 INFO @ Wed, 08 Dec 2021 15:41:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:41:31: #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 15:41:31: #1 tags after filtering in treatment: 3437289 INFO @ Wed, 08 Dec 2021 15:41:31: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 08 Dec 2021 15:41:31: #1 finished! INFO @ Wed, 08 Dec 2021 15:41:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:41:32: #2 number of paired peaks: 1076 INFO @ Wed, 08 Dec 2021 15:41:32: start model_add_line... INFO @ Wed, 08 Dec 2021 15:41:32: start X-correlation... INFO @ Wed, 08 Dec 2021 15:41:32: end of X-cor INFO @ Wed, 08 Dec 2021 15:41:32: #2 finished! INFO @ Wed, 08 Dec 2021 15:41:32: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 15:41:32: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 15:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.10_model.r WARNING @ Wed, 08 Dec 2021 15:41:32: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:41:32: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 15:41:32: #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 15:41:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:41:35: 13000000 INFO @ Wed, 08 Dec 2021 15:41:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:41:44: 14000000 INFO @ Wed, 08 Dec 2021 15:41:44: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:41:44: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:41:44: #1 total tags in treatment: 4832890 INFO @ Wed, 08 Dec 2021 15:41:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:41:44: #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 15:41:44: #1 tags after filtering in treatment: 3437289 INFO @ Wed, 08 Dec 2021 15:41:44: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 08 Dec 2021 15:41:44: #1 finished! INFO @ Wed, 08 Dec 2021 15:41:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:41:44: #2 number of paired peaks: 1076 INFO @ Wed, 08 Dec 2021 15:41:44: start model_add_line... INFO @ Wed, 08 Dec 2021 15:41:44: start X-correlation... INFO @ Wed, 08 Dec 2021 15:41:44: end of X-cor INFO @ Wed, 08 Dec 2021 15:41:44: #2 finished! INFO @ Wed, 08 Dec 2021 15:41:44: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 15:41:44: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 15:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.20_model.r WARNING @ Wed, 08 Dec 2021 15:41:44: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:41:44: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 15:41:44: #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 15:41:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:41:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:41:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:41:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.10_summits.bed INFO @ Wed, 08 Dec 2021 15:41:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:41:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641202/SRX10641202.20_summits.bed INFO @ Wed, 08 Dec 2021 15:41:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 1 millis CompletedMACS2peakCalling