Job ID = 14158378 SRX = SRX10641175 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T07:31:30 prefetch.2.10.7: 1) Downloading 'SRR14280103'... 2021-12-08T07:31:30 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T07:57:49 prefetch.2.10.7: HTTPS download succeed 2021-12-08T07:57:49 prefetch.2.10.7: 1) 'SRR14280103' was downloaded successfully 2021-12-08T07:57:49 prefetch.2.10.7: 'SRR14280103' has 0 unresolved dependencies Read 14272621 spots for SRR14280103/SRR14280103.sra Written 14272621 spots for SRR14280103/SRR14280103.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159042 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:11 14272621 reads; of these: 14272621 (100.00%) were paired; of these: 6049034 (42.38%) aligned concordantly 0 times 6946122 (48.67%) aligned concordantly exactly 1 time 1277465 (8.95%) aligned concordantly >1 times ---- 6049034 pairs aligned concordantly 0 times; of these: 1569843 (25.95%) aligned discordantly 1 time ---- 4479191 pairs aligned 0 times concordantly or discordantly; of these: 8958382 mates make up the pairs; of these: 8302142 (92.67%) aligned 0 times 310507 (3.47%) aligned exactly 1 time 345733 (3.86%) aligned >1 times 70.92% overall alignment rate Time searching: 00:22:11 Overall time: 00:22:11 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] 1197457 / 9750854 = 0.1228 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 17:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.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 17:31:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:31:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:31:11: 1000000 INFO @ Wed, 08 Dec 2021 17:31:20: 2000000 INFO @ Wed, 08 Dec 2021 17:31:29: 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 17:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.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 17:31:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:31:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:31:39: 4000000 INFO @ Wed, 08 Dec 2021 17:31:42: 1000000 INFO @ Wed, 08 Dec 2021 17:31:48: 5000000 INFO @ Wed, 08 Dec 2021 17:31:51: 2000000 INFO @ Wed, 08 Dec 2021 17:31:58: 6000000 INFO @ Wed, 08 Dec 2021 17:32:00: 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 @ Wed, 08 Dec 2021 17:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.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 17:32:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:32:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:32:08: 7000000 INFO @ Wed, 08 Dec 2021 17:32:09: 4000000 INFO @ Wed, 08 Dec 2021 17:32:12: 1000000 INFO @ Wed, 08 Dec 2021 17:32:18: 8000000 INFO @ Wed, 08 Dec 2021 17:32:18: 5000000 INFO @ Wed, 08 Dec 2021 17:32:22: 2000000 INFO @ Wed, 08 Dec 2021 17:32:27: 6000000 INFO @ Wed, 08 Dec 2021 17:32:28: 9000000 INFO @ Wed, 08 Dec 2021 17:32:33: 3000000 INFO @ Wed, 08 Dec 2021 17:32:37: 7000000 INFO @ Wed, 08 Dec 2021 17:32:37: 10000000 INFO @ Wed, 08 Dec 2021 17:32:42: 4000000 INFO @ Wed, 08 Dec 2021 17:32:46: 8000000 INFO @ Wed, 08 Dec 2021 17:32:47: 11000000 INFO @ Wed, 08 Dec 2021 17:32:52: 5000000 INFO @ Wed, 08 Dec 2021 17:32:55: 9000000 INFO @ Wed, 08 Dec 2021 17:32:57: 12000000 INFO @ Wed, 08 Dec 2021 17:33:02: 6000000 INFO @ Wed, 08 Dec 2021 17:33:04: 10000000 INFO @ Wed, 08 Dec 2021 17:33:07: 13000000 INFO @ Wed, 08 Dec 2021 17:33:12: 7000000 INFO @ Wed, 08 Dec 2021 17:33:13: 11000000 INFO @ Wed, 08 Dec 2021 17:33:17: 14000000 INFO @ Wed, 08 Dec 2021 17:33:21: 8000000 INFO @ Wed, 08 Dec 2021 17:33:22: 12000000 INFO @ Wed, 08 Dec 2021 17:33:27: 15000000 INFO @ Wed, 08 Dec 2021 17:33:31: 9000000 INFO @ Wed, 08 Dec 2021 17:33:31: 13000000 INFO @ Wed, 08 Dec 2021 17:33:37: 16000000 INFO @ Wed, 08 Dec 2021 17:33:40: 14000000 INFO @ Wed, 08 Dec 2021 17:33:41: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:33:46: 17000000 INFO @ Wed, 08 Dec 2021 17:33:49: 15000000 INFO @ Wed, 08 Dec 2021 17:33:51: 11000000 INFO @ Wed, 08 Dec 2021 17:33:55: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:33:55: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:33:55: #1 total tags in treatment: 7175278 INFO @ Wed, 08 Dec 2021 17:33:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:33:55: #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 17:33:55: #1 tags after filtering in treatment: 6664874 INFO @ Wed, 08 Dec 2021 17:33:55: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:33:55: #1 finished! INFO @ Wed, 08 Dec 2021 17:33:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:33:55: #2 number of paired peaks: 482 WARNING @ Wed, 08 Dec 2021 17:33:55: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Wed, 08 Dec 2021 17:33:55: start model_add_line... INFO @ Wed, 08 Dec 2021 17:33:55: start X-correlation... INFO @ Wed, 08 Dec 2021 17:33:55: end of X-cor INFO @ Wed, 08 Dec 2021 17:33:55: #2 finished! INFO @ Wed, 08 Dec 2021 17:33:55: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:33:55: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.05_model.r WARNING @ Wed, 08 Dec 2021 17:33:55: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:33:55: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:33:55: #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 17:33:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:33:58: 16000000 INFO @ Wed, 08 Dec 2021 17:34:00: 12000000 INFO @ Wed, 08 Dec 2021 17:34:07: 17000000 INFO @ Wed, 08 Dec 2021 17:34:10: 13000000 INFO @ Wed, 08 Dec 2021 17:34:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:34:15: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:34:15: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:34:15: #1 total tags in treatment: 7175278 INFO @ Wed, 08 Dec 2021 17:34:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:34:15: #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 17:34:15: #1 tags after filtering in treatment: 6664874 INFO @ Wed, 08 Dec 2021 17:34:15: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:34:15: #1 finished! INFO @ Wed, 08 Dec 2021 17:34:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:34:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:34:15: #2 number of paired peaks: 482 WARNING @ Wed, 08 Dec 2021 17:34:15: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Wed, 08 Dec 2021 17:34:15: start model_add_line... INFO @ Wed, 08 Dec 2021 17:34:15: start X-correlation... INFO @ Wed, 08 Dec 2021 17:34:15: end of X-cor INFO @ Wed, 08 Dec 2021 17:34:15: #2 finished! INFO @ Wed, 08 Dec 2021 17:34:15: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:34:15: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.10_model.r WARNING @ Wed, 08 Dec 2021 17:34:15: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:34:15: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:34:15: #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 17:34:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:34:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.05_summits.bed INFO @ Wed, 08 Dec 2021 17:34:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:34:19: 14000000 INFO @ Wed, 08 Dec 2021 17:34:28: 15000000 INFO @ Wed, 08 Dec 2021 17:34:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.10_summits.bed INFO @ Wed, 08 Dec 2021 17:34:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:34:37: 16000000 INFO @ Wed, 08 Dec 2021 17:34:46: 17000000 INFO @ Wed, 08 Dec 2021 17:34:54: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:34:54: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:34:54: #1 total tags in treatment: 7175278 INFO @ Wed, 08 Dec 2021 17:34:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:34:54: #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 17:34:54: #1 tags after filtering in treatment: 6664874 INFO @ Wed, 08 Dec 2021 17:34:54: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:34:54: #1 finished! INFO @ Wed, 08 Dec 2021 17:34:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:34:54: #2 number of paired peaks: 482 WARNING @ Wed, 08 Dec 2021 17:34:54: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Wed, 08 Dec 2021 17:34:54: start model_add_line... INFO @ Wed, 08 Dec 2021 17:34:55: start X-correlation... INFO @ Wed, 08 Dec 2021 17:34:55: end of X-cor INFO @ Wed, 08 Dec 2021 17:34:55: #2 finished! INFO @ Wed, 08 Dec 2021 17:34:55: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:34:55: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.20_model.r WARNING @ Wed, 08 Dec 2021 17:34:55: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:34:55: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:34:55: #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 17:34:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:35:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:35:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:35:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641175/SRX10641175.20_summits.bed INFO @ Wed, 08 Dec 2021 17:35:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling