[2024-01-24 12:27:19,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference
[2024-01-24 12:27:20,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,521] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,521] [INFO] Running command: gunzip -c /var/lib/cwl/stg32ec8abb-8673-43b7-8c99-cede35c42ff4/GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna.gz | prodigal -d GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/cds.fna -a GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:34,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:34,054] [INFO] Task started: HMMsearch
[2024-01-24 12:27:34,055] [INFO] Running command: hmmsearch --tblout GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference/reference_markers.hmm GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:34,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:34,348] [INFO] Found 6/6 markers.
[2024-01-24 12:27:34,401] [INFO] Query marker FASTA was written to GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/markers.fasta
[2024-01-24 12:27:34,402] [INFO] Task started: Blastn
[2024-01-24 12:27:34,402] [INFO] Running command: blastn -query GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference/reference_markers.fasta -out GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:35,024] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:35,029] [INFO] Selected 11 target genomes.
[2024-01-24 12:27:35,029] [INFO] Target genome list was writen to GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:35,055] [INFO] Task started: fastANI
[2024-01-24 12:27:35,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ec8abb-8673-43b7-8c99-cede35c42ff4/GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna.gz --refList GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/target_genomes.txt --output GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:45,674] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:45,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:45,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:45,685] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:27:45,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:27:45,685] [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
Pseudodesulfovibrio profundus	strain=500-1	GCA_900217235.1	57320	57320	type	True	100.0	1402	1405	95	conclusive
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	84.6315	53	1405	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	79.0466	383	1405	95	below_threshold
Pseudodesulfovibrio piezophilus	strain=type strain: C1TLV30	GCA_000341895.1	879567	879567	type	True	78.6341	263	1405	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	78.6006	319	1405	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	78.5835	308	1405	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	78.3732	341	1405	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	78.1017	290	1405	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	77.7602	241	1405	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	77.443	202	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:45,687] [INFO] DFAST Taxonomy check result was written to GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:45,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:45,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:45,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference/checkm_data
[2024-01-24 12:27:45,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:45,727] [INFO] Task started: CheckM
[2024-01-24 12:27:45,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/checkm_input GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/checkm_result
[2024-01-24 12:28:28,318] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:28,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:28,344] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:28,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:28,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/markers.fasta)
[2024-01-24 12:28:28,345] [INFO] Task started: Blastn
[2024-01-24 12:28:28,346] [INFO] Running command: blastn -query GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c2e975a-147a-46eb-9bdb-0cfa8bf94427/dqc_reference/reference_markers_gtdb.fasta -out GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:29,234] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:29,241] [INFO] Selected 12 target genomes.
[2024-01-24 12:28:29,241] [INFO] Target genome list was writen to GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:29,315] [INFO] Task started: fastANI
[2024-01-24 12:28:29,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ec8abb-8673-43b7-8c99-cede35c42ff4/GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna.gz --refList GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:39,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:39,162] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:39,162] [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_900217235.1	s__Pseudodesulfovibrio profundus	100.0	1402	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	98.02	97.98	0.88	0.83	5	conclusive
GCF_012516435.1	s__Pseudodesulfovibrio sp012516435	79.3664	392	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762795.1	s__Pseudodesulfovibrio cashew	79.0932	384	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341895.1	s__Pseudodesulfovibrio piezophilus	78.6748	265	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563225.1	s__Pseudodesulfovibrio indicus	78.627	316	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016744135.1	s__Pseudodesulfovibrio sp016744135	78.1649	244	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189295.2	s__Pseudodesulfovibrio mercurii	78.1338	293	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874525.1	s__Pseudodesulfovibrio hydrargyri	78.08	291	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709315.1	s__Pseudodesulfovibrio sp015709315	77.9855	278	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468615.1	s__Pseudodesulfovibrio sp010468615	77.9503	229	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729555.1	s__Pseudodesulfovibrio sp009729555	77.7566	240	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008830225.1	s__Pseudodesulfovibrio senegalensis	77.266	165	1405	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:39,164] [INFO] GTDB search result was written to GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:39,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:39,170] [INFO] DFAST_QC result json was written to GCF_900217235.1_DPRO_PRJEB22548_v1_genomic.fna/dqc_result.json
[2024-01-24 12:28:39,170] [INFO] DFAST_QC completed!
[2024-01-24 12:28:39,170] [INFO] Total running time: 0h1m20s