Job ID = 12265635 SRX = SRX7246273 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: 00:44:01 33208398 reads; of these: 33208398 (100.00%) were paired; of these: 22092198 (66.53%) aligned concordantly 0 times 9918274 (29.87%) aligned concordantly exactly 1 time 1197926 (3.61%) aligned concordantly >1 times ---- 22092198 pairs aligned concordantly 0 times; of these: 4824723 (21.84%) aligned discordantly 1 time ---- 17267475 pairs aligned 0 times concordantly or discordantly; of these: 34534950 mates make up the pairs; of these: 32784217 (94.93%) aligned 0 times 867969 (2.51%) aligned exactly 1 time 882764 (2.56%) aligned >1 times 50.64% overall alignment rate Time searching: 00:44:01 Overall time: 00:44:01 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 28 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] 8456400 / 15815865 = 0.5347 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 08:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.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 08:50:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:50:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:50:45: 1000000 INFO @ Sat, 03 Apr 2021 08:50:54: 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 08:51:04: 3000000 INFO @ Sat, 03 Apr 2021 08:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.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 08:51:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:51:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:51:15: 4000000 INFO @ Sat, 03 Apr 2021 08:51:15: 1000000 INFO @ Sat, 03 Apr 2021 08:51:25: 2000000 INFO @ Sat, 03 Apr 2021 08:51:25: 5000000 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 08:51:35: 3000000 INFO @ Sat, 03 Apr 2021 08:51:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.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 08:51:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:51:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:51:35: 6000000 INFO @ Sat, 03 Apr 2021 08:51:45: 4000000 INFO @ Sat, 03 Apr 2021 08:51:46: 1000000 INFO @ Sat, 03 Apr 2021 08:51:46: 7000000 INFO @ Sat, 03 Apr 2021 08:51:55: 5000000 INFO @ Sat, 03 Apr 2021 08:51:56: 2000000 INFO @ Sat, 03 Apr 2021 08:51:56: 8000000 INFO @ Sat, 03 Apr 2021 08:52:05: 6000000 INFO @ Sat, 03 Apr 2021 08:52:07: 9000000 INFO @ Sat, 03 Apr 2021 08:52:07: 3000000 INFO @ Sat, 03 Apr 2021 08:52:15: 7000000 INFO @ Sat, 03 Apr 2021 08:52:17: 10000000 INFO @ Sat, 03 Apr 2021 08:52:18: 4000000 INFO @ Sat, 03 Apr 2021 08:52:25: 8000000 INFO @ Sat, 03 Apr 2021 08:52:27: 11000000 INFO @ Sat, 03 Apr 2021 08:52:29: 5000000 INFO @ Sat, 03 Apr 2021 08:52:35: 9000000 INFO @ Sat, 03 Apr 2021 08:52:37: 12000000 INFO @ Sat, 03 Apr 2021 08:52:39: 6000000 INFO @ Sat, 03 Apr 2021 08:52:45: 10000000 INFO @ Sat, 03 Apr 2021 08:52:47: 13000000 INFO @ Sat, 03 Apr 2021 08:52:49: 7000000 INFO @ Sat, 03 Apr 2021 08:52:55: 11000000 INFO @ Sat, 03 Apr 2021 08:52:58: 14000000 INFO @ Sat, 03 Apr 2021 08:53:00: 8000000 INFO @ Sat, 03 Apr 2021 08:53:05: 12000000 INFO @ Sat, 03 Apr 2021 08:53:08: 15000000 INFO @ Sat, 03 Apr 2021 08:53:11: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:53:15: 13000000 INFO @ Sat, 03 Apr 2021 08:53:19: 16000000 INFO @ Sat, 03 Apr 2021 08:53:21: 10000000 INFO @ Sat, 03 Apr 2021 08:53:25: 14000000 INFO @ Sat, 03 Apr 2021 08:53:26: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:53:26: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:53:26: #1 total tags in treatment: 4953419 INFO @ Sat, 03 Apr 2021 08:53:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:53:26: #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 08:53:26: #1 tags after filtering in treatment: 3751525 INFO @ Sat, 03 Apr 2021 08:53:26: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:53:26: #1 finished! INFO @ Sat, 03 Apr 2021 08:53:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:53:26: #2 number of paired peaks: 2273 INFO @ Sat, 03 Apr 2021 08:53:26: start model_add_line... INFO @ Sat, 03 Apr 2021 08:53:26: start X-correlation... INFO @ Sat, 03 Apr 2021 08:53:27: end of X-cor INFO @ Sat, 03 Apr 2021 08:53:27: #2 finished! INFO @ Sat, 03 Apr 2021 08:53:27: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Apr 2021 08:53:27: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 03 Apr 2021 08:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.05_model.r WARNING @ Sat, 03 Apr 2021 08:53:27: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:53:27: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 03 Apr 2021 08:53:27: #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 08:53:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:53:31: 11000000 INFO @ Sat, 03 Apr 2021 08:53:35: 15000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:53:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:53:41: 12000000 INFO @ Sat, 03 Apr 2021 08:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.05_summits.bed INFO @ Sat, 03 Apr 2021 08:53:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4402 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:53:45: 16000000 INFO @ Sat, 03 Apr 2021 08:53:52: 13000000 INFO @ Sat, 03 Apr 2021 08:53:52: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:53:52: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:53:52: #1 total tags in treatment: 4953419 INFO @ Sat, 03 Apr 2021 08:53:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:53:52: #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 08:53:53: #1 tags after filtering in treatment: 3751525 INFO @ Sat, 03 Apr 2021 08:53:53: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:53:53: #1 finished! INFO @ Sat, 03 Apr 2021 08:53:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:53:53: #2 number of paired peaks: 2273 INFO @ Sat, 03 Apr 2021 08:53:53: start model_add_line... INFO @ Sat, 03 Apr 2021 08:53:53: start X-correlation... INFO @ Sat, 03 Apr 2021 08:53:53: end of X-cor INFO @ Sat, 03 Apr 2021 08:53:53: #2 finished! INFO @ Sat, 03 Apr 2021 08:53:53: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Apr 2021 08:53:53: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 03 Apr 2021 08:53:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.10_model.r WARNING @ Sat, 03 Apr 2021 08:53:53: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:53:53: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 03 Apr 2021 08:53:53: #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 08:53:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:02: 14000000 INFO @ Sat, 03 Apr 2021 08:54:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:54:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.10_summits.bed INFO @ Sat, 03 Apr 2021 08:54:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2638 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:54:12: 15000000 INFO @ Sat, 03 Apr 2021 08:54:22: 16000000 INFO @ Sat, 03 Apr 2021 08:54:29: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:54:29: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:54:29: #1 total tags in treatment: 4953419 INFO @ Sat, 03 Apr 2021 08:54:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:54:29: #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 08:54:29: #1 tags after filtering in treatment: 3751525 INFO @ Sat, 03 Apr 2021 08:54:29: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:54:29: #1 finished! INFO @ Sat, 03 Apr 2021 08:54:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:54:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:54:29: #2 number of paired peaks: 2273 INFO @ Sat, 03 Apr 2021 08:54:29: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:29: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:29: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:29: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:29: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Apr 2021 08:54:29: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 03 Apr 2021 08:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.20_model.r WARNING @ Sat, 03 Apr 2021 08:54:29: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:54:29: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 03 Apr 2021 08:54:29: #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 08:54:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246273/SRX7246273.20_summits.bed INFO @ Sat, 03 Apr 2021 08:54:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1204 records, 4 fields): 4 millis CompletedMACS2peakCalling