Job ID = 12265836 SRX = SRX2333004 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: 02:10:52 31364016 reads; of these: 31364016 (100.00%) were paired; of these: 15224912 (48.54%) aligned concordantly 0 times 3361677 (10.72%) aligned concordantly exactly 1 time 12777427 (40.74%) aligned concordantly >1 times ---- 15224912 pairs aligned concordantly 0 times; of these: 1212554 (7.96%) aligned discordantly 1 time ---- 14012358 pairs aligned 0 times concordantly or discordantly; of these: 28024716 mates make up the pairs; of these: 23843513 (85.08%) aligned 0 times 836280 (2.98%) aligned exactly 1 time 3344923 (11.94%) aligned >1 times 61.99% overall alignment rate Time searching: 02:10:52 Overall time: 02:10:52 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] 8586910 / 17199774 = 0.4992 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 10:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.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 10:59:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:59:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:59:21: 1000000 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 10:59:35: 2000000 INFO @ Sat, 03 Apr 2021 10:59:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.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 10:59:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:59:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:59:49: 1000000 INFO @ Sat, 03 Apr 2021 10:59:50: 3000000 INFO @ Sat, 03 Apr 2021 11:00:01: 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 11:00:06: 4000000 INFO @ Sat, 03 Apr 2021 11:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.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 11:00:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 11:00:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 11:00:14: 3000000 INFO @ Sat, 03 Apr 2021 11:00:17: 1000000 INFO @ Sat, 03 Apr 2021 11:00:21: 5000000 INFO @ Sat, 03 Apr 2021 11:00:26: 4000000 INFO @ Sat, 03 Apr 2021 11:00:28: 2000000 INFO @ Sat, 03 Apr 2021 11:00:37: 6000000 INFO @ Sat, 03 Apr 2021 11:00:38: 5000000 INFO @ Sat, 03 Apr 2021 11:00:38: 3000000 INFO @ Sat, 03 Apr 2021 11:00:49: 4000000 INFO @ Sat, 03 Apr 2021 11:00:51: 6000000 INFO @ Sat, 03 Apr 2021 11:00:53: 7000000 INFO @ Sat, 03 Apr 2021 11:01:00: 5000000 INFO @ Sat, 03 Apr 2021 11:01:03: 7000000 INFO @ Sat, 03 Apr 2021 11:01:07: 8000000 INFO @ Sat, 03 Apr 2021 11:01:10: 6000000 INFO @ Sat, 03 Apr 2021 11:01:15: 8000000 INFO @ Sat, 03 Apr 2021 11:01:21: 7000000 INFO @ Sat, 03 Apr 2021 11:01:22: 9000000 INFO @ Sat, 03 Apr 2021 11:01:27: 9000000 INFO @ Sat, 03 Apr 2021 11:01:31: 8000000 INFO @ Sat, 03 Apr 2021 11:01:37: 10000000 INFO @ Sat, 03 Apr 2021 11:01:39: 10000000 INFO @ Sat, 03 Apr 2021 11:01:42: 9000000 INFO @ Sat, 03 Apr 2021 11:01:51: 11000000 INFO @ Sat, 03 Apr 2021 11:01:52: 10000000 INFO @ Sat, 03 Apr 2021 11:01:53: 11000000 INFO @ Sat, 03 Apr 2021 11:02:02: 11000000 INFO @ Sat, 03 Apr 2021 11:02:03: 12000000 INFO @ Sat, 03 Apr 2021 11:02:09: 12000000 INFO @ Sat, 03 Apr 2021 11:02:12: 12000000 INFO @ Sat, 03 Apr 2021 11:02:15: 13000000 INFO @ Sat, 03 Apr 2021 11:02:23: 13000000 INFO @ Sat, 03 Apr 2021 11:02:24: 13000000 INFO @ Sat, 03 Apr 2021 11:02:27: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 11:02:33: 14000000 INFO @ Sat, 03 Apr 2021 11:02:39: 15000000 INFO @ Sat, 03 Apr 2021 11:02:39: 14000000 INFO @ Sat, 03 Apr 2021 11:02:44: 15000000 INFO @ Sat, 03 Apr 2021 11:02:51: 16000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 11:02:54: 15000000 INFO @ Sat, 03 Apr 2021 11:02:54: 16000000 INFO @ Sat, 03 Apr 2021 11:03:03: 17000000 INFO @ Sat, 03 Apr 2021 11:03:04: 17000000 INFO @ Sat, 03 Apr 2021 11:03:09: 16000000 INFO @ Sat, 03 Apr 2021 11:03:15: 18000000 INFO @ Sat, 03 Apr 2021 11:03:15: 18000000 INFO @ Sat, 03 Apr 2021 11:03:24: 17000000 INFO @ Sat, 03 Apr 2021 11:03:25: 19000000 INFO @ Sat, 03 Apr 2021 11:03:27: 19000000 INFO @ Sat, 03 Apr 2021 11:03:36: 20000000 INFO @ Sat, 03 Apr 2021 11:03:39: 18000000 INFO @ Sat, 03 Apr 2021 11:03:39: 20000000 INFO @ Sat, 03 Apr 2021 11:03:46: 21000000 INFO @ Sat, 03 Apr 2021 11:03:51: 21000000 INFO @ Sat, 03 Apr 2021 11:03:54: 19000000 INFO @ Sat, 03 Apr 2021 11:03:54: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 11:03:54: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 11:03:54: #1 total tags in treatment: 7900753 INFO @ Sat, 03 Apr 2021 11:03:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 11:03:54: #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 11:03:54: #1 tags after filtering in treatment: 3315521 INFO @ Sat, 03 Apr 2021 11:03:54: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 03 Apr 2021 11:03:54: #1 finished! INFO @ Sat, 03 Apr 2021 11:03:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 11:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 11:03:55: #2 number of paired peaks: 5796 INFO @ Sat, 03 Apr 2021 11:03:55: start model_add_line... INFO @ Sat, 03 Apr 2021 11:03:55: start X-correlation... INFO @ Sat, 03 Apr 2021 11:03:55: end of X-cor INFO @ Sat, 03 Apr 2021 11:03:55: #2 finished! INFO @ Sat, 03 Apr 2021 11:03:55: #2 predicted fragment length is 143 bps INFO @ Sat, 03 Apr 2021 11:03:55: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 03 Apr 2021 11:03:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.20_model.r WARNING @ Sat, 03 Apr 2021 11:03:55: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 11:03:55: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 03 Apr 2021 11:03:55: #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 11:03:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 11:03:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 11:04:00: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 11:04:00: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 11:04:00: #1 total tags in treatment: 7900753 INFO @ Sat, 03 Apr 2021 11:04:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 11:04:00: #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 11:04:00: #1 tags after filtering in treatment: 3315521 INFO @ Sat, 03 Apr 2021 11:04:00: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 03 Apr 2021 11:04:00: #1 finished! INFO @ Sat, 03 Apr 2021 11:04:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 11:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 11:04:01: #2 number of paired peaks: 5796 INFO @ Sat, 03 Apr 2021 11:04:01: start model_add_line... INFO @ Sat, 03 Apr 2021 11:04:01: start X-correlation... INFO @ Sat, 03 Apr 2021 11:04:01: end of X-cor INFO @ Sat, 03 Apr 2021 11:04:01: #2 finished! INFO @ Sat, 03 Apr 2021 11:04:01: #2 predicted fragment length is 143 bps INFO @ Sat, 03 Apr 2021 11:04:01: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 03 Apr 2021 11:04:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.10_model.r WARNING @ Sat, 03 Apr 2021 11:04:01: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 11:04:01: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 03 Apr 2021 11:04:01: #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 11:04:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 11:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 11:04:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 11:04:08: 20000000 INFO @ Sat, 03 Apr 2021 11:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.20_peaks.xls INFO @ Sat, 03 Apr 2021 11:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 11:04:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.20_summits.bed INFO @ Sat, 03 Apr 2021 11:04:12: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2471 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 11:04:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 11:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.10_peaks.xls INFO @ Sat, 03 Apr 2021 11:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 11:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.10_summits.bed INFO @ Sat, 03 Apr 2021 11:04:19: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4948 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 11:04:22: 21000000 INFO @ Sat, 03 Apr 2021 11:04:32: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 11:04:32: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 11:04:32: #1 total tags in treatment: 7900753 INFO @ Sat, 03 Apr 2021 11:04:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 11:04:32: #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 11:04:32: #1 tags after filtering in treatment: 3315521 INFO @ Sat, 03 Apr 2021 11:04:32: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 03 Apr 2021 11:04:32: #1 finished! INFO @ Sat, 03 Apr 2021 11:04:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 11:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 11:04:33: #2 number of paired peaks: 5796 INFO @ Sat, 03 Apr 2021 11:04:33: start model_add_line... INFO @ Sat, 03 Apr 2021 11:04:33: start X-correlation... INFO @ Sat, 03 Apr 2021 11:04:33: end of X-cor INFO @ Sat, 03 Apr 2021 11:04:33: #2 finished! INFO @ Sat, 03 Apr 2021 11:04:33: #2 predicted fragment length is 143 bps INFO @ Sat, 03 Apr 2021 11:04:33: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 03 Apr 2021 11:04:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.05_model.r WARNING @ Sat, 03 Apr 2021 11:04:33: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 11:04:33: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 03 Apr 2021 11:04:33: #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 11:04:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 11:04:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 11:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 11:04:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.05_peaks.xls INFO @ Sat, 03 Apr 2021 11:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 11:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2333004/SRX2333004.05_summits.bed INFO @ Sat, 03 Apr 2021 11:04:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7063 records, 4 fields): 14 millis CompletedMACS2peakCalling