Job ID = 5720910 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:03:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T18:03:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T18:06:08 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T18:06:08 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T18:07:22 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 22,056,021 reads read : 22,056,021 reads written : 22,056,021 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:07:25 22056021 reads; of these: 22056021 (100.00%) were unpaired; of these: 7604685 (34.48%) aligned 0 times 9715738 (44.05%) aligned exactly 1 time 4735598 (21.47%) aligned >1 times 65.52% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6622726 / 14451336 = 0.4583 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 03:28:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 03:28:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:28:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:28:56: 1000000 INFO @ Thu, 16 Apr 2020 03:29:01: 2000000 INFO @ Thu, 16 Apr 2020 03:29:06: 3000000 INFO @ Thu, 16 Apr 2020 03:29:11: 4000000 INFO @ Thu, 16 Apr 2020 03:29:16: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 03:29:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 03:29:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:29:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:29:21: 6000000 INFO @ Thu, 16 Apr 2020 03:29:26: 1000000 INFO @ Thu, 16 Apr 2020 03:29:27: 7000000 INFO @ Thu, 16 Apr 2020 03:29:31: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:29:31: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:29:31: #1 total tags in treatment: 7828610 INFO @ Thu, 16 Apr 2020 03:29:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:29:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:29:31: #1 tags after filtering in treatment: 7828610 INFO @ Thu, 16 Apr 2020 03:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:29:31: #1 finished! INFO @ Thu, 16 Apr 2020 03:29:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:29:32: 2000000 INFO @ Thu, 16 Apr 2020 03:29:32: #2 number of paired peaks: 273 WARNING @ Thu, 16 Apr 2020 03:29:32: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Thu, 16 Apr 2020 03:29:32: start model_add_line... INFO @ Thu, 16 Apr 2020 03:29:32: start X-correlation... INFO @ Thu, 16 Apr 2020 03:29:32: end of X-cor INFO @ Thu, 16 Apr 2020 03:29:32: #2 finished! INFO @ Thu, 16 Apr 2020 03:29:32: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:29:32: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.05_model.r WARNING @ Thu, 16 Apr 2020 03:29:32: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:29:32: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:29:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:29:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:29:37: 3000000 INFO @ Thu, 16 Apr 2020 03:29:42: 4000000 INFO @ Thu, 16 Apr 2020 03:29:47: 5000000 INFO @ Thu, 16 Apr 2020 03:29:48: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 03:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Apr 2020 03:29:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:29:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:29:52: 6000000 INFO @ Thu, 16 Apr 2020 03:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.05_summits.bed INFO @ Thu, 16 Apr 2020 03:29:56: Done! INFO @ Thu, 16 Apr 2020 03:29:58: 7000000 INFO @ Thu, 16 Apr 2020 03:29:58: 1000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1955 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:30:02: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:30:02: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:30:02: #1 total tags in treatment: 7828610 INFO @ Thu, 16 Apr 2020 03:30:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:30:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:30:02: #1 tags after filtering in treatment: 7828610 INFO @ Thu, 16 Apr 2020 03:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:30:02: #1 finished! INFO @ Thu, 16 Apr 2020 03:30:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:30:03: #2 number of paired peaks: 273 WARNING @ Thu, 16 Apr 2020 03:30:03: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Thu, 16 Apr 2020 03:30:03: start model_add_line... INFO @ Thu, 16 Apr 2020 03:30:03: start X-correlation... INFO @ Thu, 16 Apr 2020 03:30:03: end of X-cor INFO @ Thu, 16 Apr 2020 03:30:03: #2 finished! INFO @ Thu, 16 Apr 2020 03:30:03: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:30:03: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:30:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.10_model.r WARNING @ Thu, 16 Apr 2020 03:30:03: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:30:03: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:30:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:30:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:30:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:30:04: 2000000 INFO @ Thu, 16 Apr 2020 03:30:11: 3000000 INFO @ Thu, 16 Apr 2020 03:30:16: 4000000 INFO @ Thu, 16 Apr 2020 03:30:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:30:22: 5000000 INFO @ Thu, 16 Apr 2020 03:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.10_summits.bed INFO @ Thu, 16 Apr 2020 03:30:27: Done! INFO @ Thu, 16 Apr 2020 03:30:28: 6000000 pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:30:34: 7000000 INFO @ Thu, 16 Apr 2020 03:30:39: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:30:39: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:30:39: #1 total tags in treatment: 7828610 INFO @ Thu, 16 Apr 2020 03:30:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:30:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:30:39: #1 tags after filtering in treatment: 7828610 INFO @ Thu, 16 Apr 2020 03:30:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:30:39: #1 finished! INFO @ Thu, 16 Apr 2020 03:30:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:30:40: #2 number of paired peaks: 273 WARNING @ Thu, 16 Apr 2020 03:30:40: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Thu, 16 Apr 2020 03:30:40: start model_add_line... INFO @ Thu, 16 Apr 2020 03:30:40: start X-correlation... INFO @ Thu, 16 Apr 2020 03:30:40: end of X-cor INFO @ Thu, 16 Apr 2020 03:30:40: #2 finished! INFO @ Thu, 16 Apr 2020 03:30:40: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:30:40: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.20_model.r WARNING @ Thu, 16 Apr 2020 03:30:40: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:30:40: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:30:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:30:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:30:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775937/SRX5775937.20_summits.bed INFO @ Thu, 16 Apr 2020 03:31:04: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。