Job ID = 14159954 SRX = SRX8845649 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: 00:50:07 47129594 reads; of these: 47129594 (100.00%) were paired; of these: 20564707 (43.63%) aligned concordantly 0 times 22546642 (47.84%) aligned concordantly exactly 1 time 4018245 (8.53%) aligned concordantly >1 times ---- 20564707 pairs aligned concordantly 0 times; of these: 4852167 (23.59%) aligned discordantly 1 time ---- 15712540 pairs aligned 0 times concordantly or discordantly; of these: 31425080 mates make up the pairs; of these: 28849272 (91.80%) aligned 0 times 1256817 (4.00%) aligned exactly 1 time 1318991 (4.20%) aligned >1 times 69.39% overall alignment rate Time searching: 00:50:08 Overall time: 00:50:08 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] 23461968 / 31086639 = 0.7547 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 @ Thu, 09 Dec 2021 01:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.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 @ Thu, 09 Dec 2021 01:56:59: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:56:59: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:57:06: 1000000 INFO @ Thu, 09 Dec 2021 01:57:13: 2000000 INFO @ Thu, 09 Dec 2021 01:57:19: 3000000 INFO @ Thu, 09 Dec 2021 01:57:26: 4000000 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 @ Thu, 09 Dec 2021 01:57:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.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 @ Thu, 09 Dec 2021 01:57:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:57:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:57:31: 5000000 INFO @ Thu, 09 Dec 2021 01:57:37: 1000000 INFO @ Thu, 09 Dec 2021 01:57:37: 6000000 INFO @ Thu, 09 Dec 2021 01:57:44: 7000000 INFO @ Thu, 09 Dec 2021 01:57:45: 2000000 INFO @ Thu, 09 Dec 2021 01:57:50: 8000000 INFO @ Thu, 09 Dec 2021 01:57:53: 3000000 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 @ Thu, 09 Dec 2021 01:57:57: 9000000 INFO @ Thu, 09 Dec 2021 01:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.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 @ Thu, 09 Dec 2021 01:57:59: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:57:59: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:58:01: 4000000 INFO @ Thu, 09 Dec 2021 01:58:04: 10000000 INFO @ Thu, 09 Dec 2021 01:58:06: 1000000 INFO @ Thu, 09 Dec 2021 01:58:09: 5000000 INFO @ Thu, 09 Dec 2021 01:58:11: 11000000 INFO @ Thu, 09 Dec 2021 01:58:13: 2000000 INFO @ Thu, 09 Dec 2021 01:58:17: 6000000 INFO @ Thu, 09 Dec 2021 01:58:17: 12000000 INFO @ Thu, 09 Dec 2021 01:58:20: 3000000 INFO @ Thu, 09 Dec 2021 01:58:24: 13000000 INFO @ Thu, 09 Dec 2021 01:58:25: 7000000 INFO @ Thu, 09 Dec 2021 01:58:27: 4000000 INFO @ Thu, 09 Dec 2021 01:58:31: 14000000 INFO @ Thu, 09 Dec 2021 01:58:32: 8000000 INFO @ Thu, 09 Dec 2021 01:58:34: 5000000 INFO @ Thu, 09 Dec 2021 01:58:37: 15000000 INFO @ Thu, 09 Dec 2021 01:58:40: 9000000 INFO @ Thu, 09 Dec 2021 01:58:40: 6000000 INFO @ Thu, 09 Dec 2021 01:58:44: 16000000 INFO @ Thu, 09 Dec 2021 01:58:47: 7000000 INFO @ Thu, 09 Dec 2021 01:58:49: 10000000 INFO @ Thu, 09 Dec 2021 01:58:51: 17000000 INFO @ Thu, 09 Dec 2021 01:58:54: 8000000 INFO @ Thu, 09 Dec 2021 01:58:57: 11000000 INFO @ Thu, 09 Dec 2021 01:58:57: 18000000 INFO @ Thu, 09 Dec 2021 01:59:00: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:59:00: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:59:00: #1 total tags in treatment: 6186317 INFO @ Thu, 09 Dec 2021 01:59:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:59:00: #1 tags after filtering in treatment: 4760326 INFO @ Thu, 09 Dec 2021 01:59:00: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 09 Dec 2021 01:59:00: #1 finished! INFO @ Thu, 09 Dec 2021 01:59:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:59:01: #2 number of paired peaks: 784 WARNING @ Thu, 09 Dec 2021 01:59:01: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Thu, 09 Dec 2021 01:59:01: start model_add_line... INFO @ Thu, 09 Dec 2021 01:59:01: start X-correlation... INFO @ Thu, 09 Dec 2021 01:59:01: end of X-cor INFO @ Thu, 09 Dec 2021 01:59:01: #2 finished! INFO @ Thu, 09 Dec 2021 01:59:01: #2 predicted fragment length is 120 bps INFO @ Thu, 09 Dec 2021 01:59:01: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 09 Dec 2021 01:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.05_model.r WARNING @ Thu, 09 Dec 2021 01:59:01: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:59:01: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 09 Dec 2021 01:59:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:59:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:59:01: 9000000 INFO @ Thu, 09 Dec 2021 01:59:05: 12000000 INFO @ Thu, 09 Dec 2021 01:59:07: 10000000 INFO @ Thu, 09 Dec 2021 01:59:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:13: 13000000 INFO @ Thu, 09 Dec 2021 01:59:13: 11000000 INFO @ Thu, 09 Dec 2021 01:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.05_summits.bed INFO @ Thu, 09 Dec 2021 01:59:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1889 records, 4 fields): 140 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:59:20: 12000000 INFO @ Thu, 09 Dec 2021 01:59:21: 14000000 INFO @ Thu, 09 Dec 2021 01:59:26: 13000000 INFO @ Thu, 09 Dec 2021 01:59:29: 15000000 INFO @ Thu, 09 Dec 2021 01:59:32: 14000000 INFO @ Thu, 09 Dec 2021 01:59:38: 16000000 INFO @ Thu, 09 Dec 2021 01:59:38: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:59:44: 16000000 INFO @ Thu, 09 Dec 2021 01:59:47: 17000000 INFO @ Thu, 09 Dec 2021 01:59:50: 17000000 INFO @ Thu, 09 Dec 2021 01:59:56: 18000000 INFO @ Thu, 09 Dec 2021 01:59:56: 18000000 INFO @ Thu, 09 Dec 2021 02:00:00: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 02:00:00: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 02:00:00: #1 total tags in treatment: 6186317 INFO @ Thu, 09 Dec 2021 02:00:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:00:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:00:00: #1 tags after filtering in treatment: 4760326 INFO @ Thu, 09 Dec 2021 02:00:00: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 09 Dec 2021 02:00:00: #1 finished! INFO @ Thu, 09 Dec 2021 02:00:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:00:00: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 02:00:00: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 02:00:00: #1 total tags in treatment: 6186317 INFO @ Thu, 09 Dec 2021 02:00:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:00:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:00:00: #1 tags after filtering in treatment: 4760326 INFO @ Thu, 09 Dec 2021 02:00:00: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 09 Dec 2021 02:00:00: #1 finished! INFO @ Thu, 09 Dec 2021 02:00:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:00:00: #2 number of paired peaks: 784 WARNING @ Thu, 09 Dec 2021 02:00:00: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Thu, 09 Dec 2021 02:00:00: start model_add_line... INFO @ Thu, 09 Dec 2021 02:00:00: start X-correlation... INFO @ Thu, 09 Dec 2021 02:00:00: end of X-cor INFO @ Thu, 09 Dec 2021 02:00:00: #2 finished! INFO @ Thu, 09 Dec 2021 02:00:00: #2 predicted fragment length is 120 bps INFO @ Thu, 09 Dec 2021 02:00:00: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 09 Dec 2021 02:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.20_model.r WARNING @ Thu, 09 Dec 2021 02:00:00: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:00:00: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 09 Dec 2021 02:00:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:00:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:00:00: #2 number of paired peaks: 784 WARNING @ Thu, 09 Dec 2021 02:00:00: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Thu, 09 Dec 2021 02:00:00: start model_add_line... INFO @ Thu, 09 Dec 2021 02:00:00: start X-correlation... INFO @ Thu, 09 Dec 2021 02:00:00: end of X-cor INFO @ Thu, 09 Dec 2021 02:00:00: #2 finished! INFO @ Thu, 09 Dec 2021 02:00:00: #2 predicted fragment length is 120 bps INFO @ Thu, 09 Dec 2021 02:00:00: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 09 Dec 2021 02:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.10_model.r WARNING @ Thu, 09 Dec 2021 02:00:00: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:00:00: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 09 Dec 2021 02:00:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:00:00: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:00:10: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:00:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.20_summits.bed INFO @ Thu, 09 Dec 2021 02:00:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (341 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845649/SRX8845649.10_summits.bed INFO @ Thu, 09 Dec 2021 02:00:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (967 records, 4 fields): 3 millis CompletedMACS2peakCalling