Job ID = 12265415 SRX = SRX2332997 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:33:00 44833479 reads; of these: 44833479 (100.00%) were paired; of these: 38360799 (85.56%) aligned concordantly 0 times 4338028 (9.68%) aligned concordantly exactly 1 time 2134652 (4.76%) aligned concordantly >1 times ---- 38360799 pairs aligned concordantly 0 times; of these: 1192650 (3.11%) aligned discordantly 1 time ---- 37168149 pairs aligned 0 times concordantly or discordantly; of these: 74336298 mates make up the pairs; of these: 73517736 (98.90%) aligned 0 times 238086 (0.32%) aligned exactly 1 time 580476 (0.78%) aligned >1 times 18.01% overall alignment rate Time searching: 00:33:01 Overall time: 00:33:01 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 8 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] 2800701 / 7599960 = 0.3685 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 07:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.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 07:37:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:37:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:37:24: 1000000 INFO @ Sat, 03 Apr 2021 07:37:36: 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 07:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.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 07:37:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:37:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:37:48: 3000000 INFO @ Sat, 03 Apr 2021 07:37:53: 1000000 INFO @ Sat, 03 Apr 2021 07:38:01: 4000000 INFO @ Sat, 03 Apr 2021 07:38:03: 2000000 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 07:38:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.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 07:38:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:38:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:38:14: 5000000 INFO @ Sat, 03 Apr 2021 07:38:14: 3000000 INFO @ Sat, 03 Apr 2021 07:38:25: 1000000 INFO @ Sat, 03 Apr 2021 07:38:27: 6000000 INFO @ Sat, 03 Apr 2021 07:38:27: 4000000 INFO @ Sat, 03 Apr 2021 07:38:37: 2000000 INFO @ Sat, 03 Apr 2021 07:38:38: 5000000 INFO @ Sat, 03 Apr 2021 07:38:39: 7000000 INFO @ Sat, 03 Apr 2021 07:38:48: 3000000 INFO @ Sat, 03 Apr 2021 07:38:50: 8000000 INFO @ Sat, 03 Apr 2021 07:38:50: 6000000 INFO @ Sat, 03 Apr 2021 07:38:58: 4000000 INFO @ Sat, 03 Apr 2021 07:39:01: 9000000 INFO @ Sat, 03 Apr 2021 07:39:04: 7000000 INFO @ Sat, 03 Apr 2021 07:39:11: 5000000 INFO @ Sat, 03 Apr 2021 07:39:12: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:39:16: 8000000 INFO @ Sat, 03 Apr 2021 07:39:18: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:39:18: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:39:18: #1 total tags in treatment: 4069852 INFO @ Sat, 03 Apr 2021 07:39:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:39:18: #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 07:39:18: #1 tags after filtering in treatment: 2864147 INFO @ Sat, 03 Apr 2021 07:39:18: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:39:18: #1 finished! INFO @ Sat, 03 Apr 2021 07:39:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:39:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:39:18: #2 number of paired peaks: 1315 INFO @ Sat, 03 Apr 2021 07:39:18: start model_add_line... INFO @ Sat, 03 Apr 2021 07:39:18: start X-correlation... INFO @ Sat, 03 Apr 2021 07:39:18: end of X-cor INFO @ Sat, 03 Apr 2021 07:39:18: #2 finished! INFO @ Sat, 03 Apr 2021 07:39:18: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Apr 2021 07:39:18: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Apr 2021 07:39:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.05_model.r WARNING @ Sat, 03 Apr 2021 07:39:18: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:39:18: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sat, 03 Apr 2021 07:39:18: #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 07:39:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:39:22: 6000000 INFO @ Sat, 03 Apr 2021 07:39:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:39:26: 9000000 INFO @ Sat, 03 Apr 2021 07:39:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:39:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:39:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.05_summits.bed INFO @ Sat, 03 Apr 2021 07:39:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3753 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:39:32: 7000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:39:36: 10000000 INFO @ Sat, 03 Apr 2021 07:39:41: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:39:41: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:39:41: #1 total tags in treatment: 4069852 INFO @ Sat, 03 Apr 2021 07:39:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:39:41: #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 07:39:42: #1 tags after filtering in treatment: 2864147 INFO @ Sat, 03 Apr 2021 07:39:42: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:39:42: #1 finished! INFO @ Sat, 03 Apr 2021 07:39:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:39:42: #2 number of paired peaks: 1315 INFO @ Sat, 03 Apr 2021 07:39:42: start model_add_line... INFO @ Sat, 03 Apr 2021 07:39:42: start X-correlation... INFO @ Sat, 03 Apr 2021 07:39:42: end of X-cor INFO @ Sat, 03 Apr 2021 07:39:42: #2 finished! INFO @ Sat, 03 Apr 2021 07:39:42: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Apr 2021 07:39:42: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Apr 2021 07:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.10_model.r WARNING @ Sat, 03 Apr 2021 07:39:42: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:39:42: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sat, 03 Apr 2021 07:39:42: #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 07:39:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:39:42: 8000000 INFO @ Sat, 03 Apr 2021 07:39:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:39:51: 9000000 INFO @ Sat, 03 Apr 2021 07:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.10_summits.bed INFO @ Sat, 03 Apr 2021 07:39:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1414 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:40:00: 10000000 INFO @ Sat, 03 Apr 2021 07:40:04: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:40:04: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:40:04: #1 total tags in treatment: 4069852 INFO @ Sat, 03 Apr 2021 07:40:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:40:04: #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 07:40:04: #1 tags after filtering in treatment: 2864147 INFO @ Sat, 03 Apr 2021 07:40:04: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:40:04: #1 finished! INFO @ Sat, 03 Apr 2021 07:40:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:40:05: #2 number of paired peaks: 1315 INFO @ Sat, 03 Apr 2021 07:40:05: start model_add_line... INFO @ Sat, 03 Apr 2021 07:40:05: start X-correlation... INFO @ Sat, 03 Apr 2021 07:40:05: end of X-cor INFO @ Sat, 03 Apr 2021 07:40:05: #2 finished! INFO @ Sat, 03 Apr 2021 07:40:05: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Apr 2021 07:40:05: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Apr 2021 07:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.20_model.r WARNING @ Sat, 03 Apr 2021 07:40:05: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:40:05: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sat, 03 Apr 2021 07:40:05: #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 07:40:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:40:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:40:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:40:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:40:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332997/SRX2332997.20_summits.bed INFO @ Sat, 03 Apr 2021 07:40:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 2 millis CompletedMACS2peakCalling