[2023-03-17 11:57:19,288] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,289] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference
[2023-03-17 11:57:20,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,887] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,887] [INFO] Running command: cat /var/lib/cwl/stgbac2de6d-5c86-409b-9acb-33a9d67a4cd6/OceanDNA-b36075.fa | prodigal -d OceanDNA-b36075/cds.fna -a OceanDNA-b36075/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:47,637] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:47,637] [INFO] Task started: HMMsearch
[2023-03-17 11:57:47,637] [INFO] Running command: hmmsearch --tblout OceanDNA-b36075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference/reference_markers.hmm OceanDNA-b36075/protein.faa > /dev/null
[2023-03-17 11:57:47,849] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:47,850] [INFO] Found 6/6 markers.
[2023-03-17 11:57:47,874] [INFO] Query marker FASTA was written to OceanDNA-b36075/markers.fasta
[2023-03-17 11:57:47,875] [INFO] Task started: Blastn
[2023-03-17 11:57:47,875] [INFO] Running command: blastn -query OceanDNA-b36075/markers.fasta -db /var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference/reference_markers.fasta -out OceanDNA-b36075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:48,719] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:48,720] [INFO] Selected 26 target genomes.
[2023-03-17 11:57:48,721] [INFO] Target genome list was writen to OceanDNA-b36075/target_genomes.txt
[2023-03-17 11:57:48,735] [INFO] Task started: fastANI
[2023-03-17 11:57:48,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac2de6d-5c86-409b-9acb-33a9d67a4cd6/OceanDNA-b36075.fa --refList OceanDNA-b36075/target_genomes.txt --output OceanDNA-b36075/fastani_result.tsv --threads 1
[2023-03-17 11:58:06,807] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:06,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:58:06,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:58:06,820] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:58:06,821] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:58:06,821] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	77.9826	382	1423	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	77.9416	407	1423	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	77.9358	374	1423	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.7871	322	1423	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.7179	333	1423	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	77.6684	351	1423	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	77.6144	298	1423	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	77.6049	341	1423	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	77.5789	334	1423	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	77.4784	288	1423	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	77.4371	291	1423	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	77.1693	224	1423	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	77.1472	196	1423	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	76.7949	202	1423	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.3337	194	1423	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	76.2234	197	1423	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2187	174	1423	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.2023	134	1423	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.1793	137	1423	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.0743	110	1423	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	76.0526	147	1423	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.9785	151	1423	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	75.9265	80	1423	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	75.1314	53	1423	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:58:06,821] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36075/tc_result.tsv
[2023-03-17 11:58:06,821] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:58:06,821] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:58:06,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference/checkm_data
[2023-03-17 11:58:06,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:58:06,828] [INFO] Task started: CheckM
[2023-03-17 11:58:06,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36075/checkm_input OceanDNA-b36075/checkm_result
[2023-03-17 11:59:13,875] [INFO] Task succeeded: CheckM
[2023-03-17 11:59:13,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:59:13,878] [INFO] ===== Completeness check finished =====
[2023-03-17 11:59:13,878] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:59:13,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36075/markers.fasta)
[2023-03-17 11:59:13,879] [INFO] Task started: Blastn
[2023-03-17 11:59:13,879] [INFO] Running command: blastn -query OceanDNA-b36075/markers.fasta -db /var/lib/cwl/stg15c9325a-c938-488a-bf38-10debdae89b0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:59:15,523] [INFO] Task succeeded: Blastn
[2023-03-17 11:59:15,524] [INFO] Selected 24 target genomes.
[2023-03-17 11:59:15,524] [INFO] Target genome list was writen to OceanDNA-b36075/target_genomes_gtdb.txt
[2023-03-17 11:59:15,624] [INFO] Task started: fastANI
[2023-03-17 11:59:15,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac2de6d-5c86-409b-9acb-33a9d67a4cd6/OceanDNA-b36075.fa --refList OceanDNA-b36075/target_genomes_gtdb.txt --output OceanDNA-b36075/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:59:31,723] [INFO] Task succeeded: fastANI
[2023-03-17 11:59:31,736] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:59:31,737] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003201205.1	s__Sinimarinibacterium flocculans	78.119	340	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	77.9974	381	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	77.9415	407	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	77.9348	374	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	77.7963	262	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	77.7374	331	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.6669	284	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	77.6533	352	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	77.6248	297	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	77.6192	340	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	77.6166	366	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	77.6095	230	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	77.5604	336	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970595.1	s__Nevskia sp903970595	77.5035	219	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364935.1	s__Panacagrimonas perspica	77.4791	288	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Panacagrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013823855.1	s__Nevskia sp013823855	77.315	289	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733765.1	s__Algiphilus aromaticivorans	77.1693	224	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Algiphilaceae;g__Algiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711245.1	s__Polycyclovorans algicola	76.7949	202	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420165.1	s__Thioalkalivibrio sp000420165	76.3915	85	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182095.1	s__Plasticicumulans acidivorans	76.3486	191	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376845.1	s__Thioalkalivibrio sp000376845	76.2765	97	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.89	99.89	0.97	0.97	2	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.2212	187	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_018825305.1	s__Sulfurisoma sp018825305	76.0473	88	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	100.00	99.99	1.00	1.00	3	-
GCA_001897745.1	s__66-26 sp001897745	76.0139	144	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26	95.0	97.97	95.98	0.93	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-17 11:59:31,737] [INFO] GTDB search result was written to OceanDNA-b36075/result_gtdb.tsv
[2023-03-17 11:59:31,737] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:59:31,739] [INFO] DFAST_QC result json was written to OceanDNA-b36075/dqc_result.json
[2023-03-17 11:59:31,739] [INFO] DFAST_QC completed!
[2023-03-17 11:59:31,740] [INFO] Total running time: 0h2m12s