[2024-01-24 14:05:16,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference
[2024-01-24 14:05:17,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,384] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,384] [INFO] Running command: gunzip -c /var/lib/cwl/stgf356c205-f23c-43cb-85d2-f79116674933/GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/cds.fna -a GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:28,839] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:28,840] [INFO] Task started: HMMsearch
[2024-01-24 14:05:28,840] [INFO] Running command: hmmsearch --tblout GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference/reference_markers.hmm GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:29,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:29,149] [INFO] Found 6/6 markers.
[2024-01-24 14:05:29,194] [INFO] Query marker FASTA was written to GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:29,194] [INFO] Task started: Blastn
[2024-01-24 14:05:29,194] [INFO] Running command: blastn -query GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference/reference_markers.fasta -out GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:29,983] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:29,991] [INFO] Selected 19 target genomes.
[2024-01-24 14:05:29,992] [INFO] Target genome list was writen to GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:30,001] [INFO] Task started: fastANI
[2024-01-24 14:05:30,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgf356c205-f23c-43cb-85d2-f79116674933/GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna.gz --refList GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:44,715] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:44,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:44,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:44,734] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:44,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:44,735] [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
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	100.0	1190	1195	95	conclusive
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	88.2727	935	1195	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	80.1096	551	1195	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	79.8042	458	1195	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	79.6506	450	1195	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.8392	465	1195	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.8144	463	1195	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.5322	409	1195	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.1334	427	1195	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.0826	394	1195	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.8466	376	1195	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.3727	234	1195	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.2943	242	1195	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.0777	267	1195	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.6139	133	1195	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.5555	132	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:44,737] [INFO] DFAST Taxonomy check result was written to GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:05:44,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:44,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:44,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference/checkm_data
[2024-01-24 14:05:44,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:44,794] [INFO] Task started: CheckM
[2024-01-24 14:05:44,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/checkm_input GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:22,456] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:22,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:22,476] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:22,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:22,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:22,477] [INFO] Task started: Blastn
[2024-01-24 14:06:22,477] [INFO] Running command: blastn -query GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg36909dae-c740-4721-ba69-623574996a3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:23,858] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:23,862] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:23,862] [INFO] Target genome list was writen to GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:23,873] [INFO] Task started: fastANI
[2024-01-24 14:06:23,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgf356c205-f23c-43cb-85d2-f79116674933/GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna.gz --refList GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:32,985] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:33,001] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:33,002] [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_900103185.1	s__Sulfitobacter litoralis	100.0	1190	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	conclusive
GCF_006064855.1	s__Sulfitobacter sp006064855	94.7197	931	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	88.2728	935	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_013282155.1	s__Sulfitobacter sp013282155	80.8233	626	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	80.5617	626	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	80.1195	551	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	80.1179	507	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.0733	395	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.6859	343	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	77.2943	242	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	77.0978	265	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:33,004] [INFO] GTDB search result was written to GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:33,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:33,009] [INFO] DFAST_QC result json was written to GCF_900103185.1_IMG-taxon_2622736527_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:33,009] [INFO] DFAST_QC completed!
[2024-01-24 14:06:33,009] [INFO] Total running time: 0h1m17s