Job ID = 14159587 SRX = SRX3180831 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE 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: 00:03:59 15884468 reads; of these: 15884468 (100.00%) were unpaired; of these: 446810 (2.81%) aligned 0 times 12812089 (80.66%) aligned exactly 1 time 2625569 (16.53%) aligned >1 times 97.19% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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_rmdupse_core] 1539954 / 15437658 = 0.0998 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 23:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.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 23:04:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:04:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:04:36: 1000000 INFO @ Wed, 08 Dec 2021 23:04:44: 2000000 INFO @ Wed, 08 Dec 2021 23:04:52: 3000000 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 23:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.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 23:04:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:04:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:05:00: 4000000 INFO @ Wed, 08 Dec 2021 23:05:05: 1000000 INFO @ Wed, 08 Dec 2021 23:05:08: 5000000 INFO @ Wed, 08 Dec 2021 23:05:13: 2000000 INFO @ Wed, 08 Dec 2021 23:05:16: 6000000 INFO @ Wed, 08 Dec 2021 23:05:21: 3000000 INFO @ Wed, 08 Dec 2021 23:05:23: 7000000 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 23:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.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 23:05:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:05:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:05:29: 4000000 INFO @ Wed, 08 Dec 2021 23:05:31: 8000000 INFO @ Wed, 08 Dec 2021 23:05:36: 1000000 INFO @ Wed, 08 Dec 2021 23:05:38: 5000000 INFO @ Wed, 08 Dec 2021 23:05:39: 9000000 INFO @ Wed, 08 Dec 2021 23:05:45: 2000000 INFO @ Wed, 08 Dec 2021 23:05:46: 6000000 INFO @ Wed, 08 Dec 2021 23:05:47: 10000000 INFO @ Wed, 08 Dec 2021 23:05:54: 7000000 INFO @ Wed, 08 Dec 2021 23:05:55: 3000000 INFO @ Wed, 08 Dec 2021 23:05:55: 11000000 INFO @ Wed, 08 Dec 2021 23:06:02: 8000000 INFO @ Wed, 08 Dec 2021 23:06:04: 12000000 INFO @ Wed, 08 Dec 2021 23:06:04: 4000000 INFO @ Wed, 08 Dec 2021 23:06:10: 9000000 INFO @ Wed, 08 Dec 2021 23:06:11: 13000000 INFO @ Wed, 08 Dec 2021 23:06:13: 5000000 INFO @ Wed, 08 Dec 2021 23:06:17: 10000000 INFO @ Wed, 08 Dec 2021 23:06:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:06:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:06:17: #1 total tags in treatment: 13897704 INFO @ Wed, 08 Dec 2021 23:06:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:06:17: #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 23:06:18: #1 tags after filtering in treatment: 13897704 INFO @ Wed, 08 Dec 2021 23:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:06:18: #1 finished! INFO @ Wed, 08 Dec 2021 23:06:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:06:19: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 23:06:19: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 23:06:19: start model_add_line... INFO @ Wed, 08 Dec 2021 23:06:19: start X-correlation... INFO @ Wed, 08 Dec 2021 23:06:19: end of X-cor INFO @ Wed, 08 Dec 2021 23:06:19: #2 finished! INFO @ Wed, 08 Dec 2021 23:06:19: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:06:19: #2 alternative fragment length(s) may be 2,47,528,569,586,589 bps INFO @ Wed, 08 Dec 2021 23:06:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.05_model.r WARNING @ Wed, 08 Dec 2021 23:06:19: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:06:19: #2 You may need to consider one of the other alternative d(s): 2,47,528,569,586,589 WARNING @ Wed, 08 Dec 2021 23:06:19: #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 23:06:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:06:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:06:21: 6000000 INFO @ Wed, 08 Dec 2021 23:06:24: 11000000 INFO @ Wed, 08 Dec 2021 23:06:30: 7000000 INFO @ Wed, 08 Dec 2021 23:06:32: 12000000 INFO @ Wed, 08 Dec 2021 23:06:38: 8000000 INFO @ Wed, 08 Dec 2021 23:06:39: 13000000 INFO @ Wed, 08 Dec 2021 23:06:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:06:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:06:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:06:46: #1 total tags in treatment: 13897704 INFO @ Wed, 08 Dec 2021 23:06:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:06:46: #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 23:06:46: #1 tags after filtering in treatment: 13897704 INFO @ Wed, 08 Dec 2021 23:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:06:46: #1 finished! INFO @ Wed, 08 Dec 2021 23:06:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:06:47: 9000000 INFO @ Wed, 08 Dec 2021 23:06:47: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 23:06:47: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 23:06:47: start model_add_line... INFO @ Wed, 08 Dec 2021 23:06:47: start X-correlation... INFO @ Wed, 08 Dec 2021 23:06:47: end of X-cor INFO @ Wed, 08 Dec 2021 23:06:47: #2 finished! INFO @ Wed, 08 Dec 2021 23:06:47: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:06:47: #2 alternative fragment length(s) may be 2,47,528,569,586,589 bps INFO @ Wed, 08 Dec 2021 23:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.10_model.r WARNING @ Wed, 08 Dec 2021 23:06:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:06:47: #2 You may need to consider one of the other alternative d(s): 2,47,528,569,586,589 WARNING @ Wed, 08 Dec 2021 23:06:47: #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 23:06:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:06:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:06:54: 10000000 INFO @ Wed, 08 Dec 2021 23:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.05_summits.bed INFO @ Wed, 08 Dec 2021 23:06:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (717 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:07:02: 11000000 INFO @ Wed, 08 Dec 2021 23:07:10: 12000000 INFO @ Wed, 08 Dec 2021 23:07:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:07:19: 13000000 INFO @ Wed, 08 Dec 2021 23:07:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:07:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:07:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.10_summits.bed INFO @ Wed, 08 Dec 2021 23:07:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:07:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:07:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:07:26: #1 total tags in treatment: 13897704 INFO @ Wed, 08 Dec 2021 23:07:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:07:26: #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 23:07:26: #1 tags after filtering in treatment: 13897704 INFO @ Wed, 08 Dec 2021 23:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:07:26: #1 finished! INFO @ Wed, 08 Dec 2021 23:07:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:07:27: #2 number of paired peaks: 328 WARNING @ Wed, 08 Dec 2021 23:07:27: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Wed, 08 Dec 2021 23:07:27: start model_add_line... INFO @ Wed, 08 Dec 2021 23:07:27: start X-correlation... INFO @ Wed, 08 Dec 2021 23:07:27: end of X-cor INFO @ Wed, 08 Dec 2021 23:07:27: #2 finished! INFO @ Wed, 08 Dec 2021 23:07:27: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:07:27: #2 alternative fragment length(s) may be 2,47,528,569,586,589 bps INFO @ Wed, 08 Dec 2021 23:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.20_model.r WARNING @ Wed, 08 Dec 2021 23:07:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:07:27: #2 You may need to consider one of the other alternative d(s): 2,47,528,569,586,589 WARNING @ Wed, 08 Dec 2021 23:07:27: #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 23:07:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:07:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:07:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180831/SRX3180831.20_summits.bed INFO @ Wed, 08 Dec 2021 23:08:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling