[2024-01-24 11:59:22,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference
[2024-01-24 11:59:25,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,640] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgec517f15-6bf9-44ee-8d43-d6adec238ac7/GCF_016820575.1_ASM1682057v1_genomic.fna.gz | prodigal -d GCF_016820575.1_ASM1682057v1_genomic.fna/cds.fna -a GCF_016820575.1_ASM1682057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:36,833] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:36,834] [INFO] Task started: HMMsearch
[2024-01-24 11:59:36,834] [INFO] Running command: hmmsearch --tblout GCF_016820575.1_ASM1682057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference/reference_markers.hmm GCF_016820575.1_ASM1682057v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:37,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:37,104] [INFO] Found 6/6 markers.
[2024-01-24 11:59:37,141] [INFO] Query marker FASTA was written to GCF_016820575.1_ASM1682057v1_genomic.fna/markers.fasta
[2024-01-24 11:59:37,141] [INFO] Task started: Blastn
[2024-01-24 11:59:37,141] [INFO] Running command: blastn -query GCF_016820575.1_ASM1682057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference/reference_markers.fasta -out GCF_016820575.1_ASM1682057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:37,978] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:37,982] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:37,983] [INFO] Target genome list was writen to GCF_016820575.1_ASM1682057v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:38,009] [INFO] Task started: fastANI
[2024-01-24 11:59:38,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgec517f15-6bf9-44ee-8d43-d6adec238ac7/GCF_016820575.1_ASM1682057v1_genomic.fna.gz --refList GCF_016820575.1_ASM1682057v1_genomic.fna/target_genomes.txt --output GCF_016820575.1_ASM1682057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:50,499] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:50,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:50,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:50,517] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:50,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:50,517] [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
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	100.0	1236	1236	95	conclusive
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	92.1852	1111	1236	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	89.7471	1036	1236	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	81.3006	776	1236	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.3214	649	1236	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	80.2453	639	1236	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.0379	614	1236	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.0118	523	1236	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.9433	532	1236	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	79.94	512	1236	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.4731	504	1236	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.472	534	1236	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.443	555	1236	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.1219	508	1236	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.6636	341	1236	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	78.5665	332	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:50,519] [INFO] DFAST Taxonomy check result was written to GCF_016820575.1_ASM1682057v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:50,519] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:50,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:50,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference/checkm_data
[2024-01-24 11:59:50,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:50,562] [INFO] Task started: CheckM
[2024-01-24 11:59:50,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820575.1_ASM1682057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820575.1_ASM1682057v1_genomic.fna/checkm_input GCF_016820575.1_ASM1682057v1_genomic.fna/checkm_result
[2024-01-24 12:00:27,274] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:27,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:27,299] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:27,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:27,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820575.1_ASM1682057v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:27,300] [INFO] Task started: Blastn
[2024-01-24 12:00:27,301] [INFO] Running command: blastn -query GCF_016820575.1_ASM1682057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635e0c89-3f81-4977-85b6-e8a0df478669/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820575.1_ASM1682057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:28,658] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:28,662] [INFO] Selected 15 target genomes.
[2024-01-24 12:00:28,662] [INFO] Target genome list was writen to GCF_016820575.1_ASM1682057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:28,672] [INFO] Task started: fastANI
[2024-01-24 12:00:28,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgec517f15-6bf9-44ee-8d43-d6adec238ac7/GCF_016820575.1_ASM1682057v1_genomic.fna.gz --refList GCF_016820575.1_ASM1682057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820575.1_ASM1682057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:40,280] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:40,293] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:40,294] [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_016820575.1	s__Marinobacter sediminum	100.0	1236	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000830985.1	s__Marinobacter similis	92.1852	1111	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871205.1	s__Marinobacter alexandrii	89.7471	1036	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_001650915.1	s__Marinobacter sp001650915	80.3544	676	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_002933295.1	s__Marinobacter flavimaris	80.3304	648	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	80.2481	637	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_000166295.1	s__Marinobacter adhaerens	80.2453	639	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900115175.1	s__Marinobacter gudaonensis	80.2352	655	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.0927	616	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	80.0393	505	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.0387	613	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	79.7367	537	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	79.6832	431	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347775.1	s__Marinobacter santoriniensis	79.4731	504	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301335.1	s__Marinobacter sp017301335	79.4671	549	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:40,295] [INFO] GTDB search result was written to GCF_016820575.1_ASM1682057v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:40,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:40,299] [INFO] DFAST_QC result json was written to GCF_016820575.1_ASM1682057v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:40,299] [INFO] DFAST_QC completed!
[2024-01-24 12:00:40,299] [INFO] Total running time: 0h1m17s