[2024-01-24 13:22:00,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference
[2024-01-24 13:22:01,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:01,848] [INFO] Task started: Prodigal
[2024-01-24 13:22:01,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg61eedc52-3e00-4727-9a55-17e5655151fd/GCF_030035605.1_ASM3003560v1_genomic.fna.gz | prodigal -d GCF_030035605.1_ASM3003560v1_genomic.fna/cds.fna -a GCF_030035605.1_ASM3003560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:17,948] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:17,949] [INFO] Task started: HMMsearch
[2024-01-24 13:22:17,949] [INFO] Running command: hmmsearch --tblout GCF_030035605.1_ASM3003560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference/reference_markers.hmm GCF_030035605.1_ASM3003560v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:18,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:18,282] [INFO] Found 6/6 markers.
[2024-01-24 13:22:18,323] [INFO] Query marker FASTA was written to GCF_030035605.1_ASM3003560v1_genomic.fna/markers.fasta
[2024-01-24 13:22:18,323] [INFO] Task started: Blastn
[2024-01-24 13:22:18,323] [INFO] Running command: blastn -query GCF_030035605.1_ASM3003560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference/reference_markers.fasta -out GCF_030035605.1_ASM3003560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:19,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:19,136] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:19,136] [INFO] Target genome list was writen to GCF_030035605.1_ASM3003560v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:19,143] [INFO] Task started: fastANI
[2024-01-24 13:22:19,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg61eedc52-3e00-4727-9a55-17e5655151fd/GCF_030035605.1_ASM3003560v1_genomic.fna.gz --refList GCF_030035605.1_ASM3003560v1_genomic.fna/target_genomes.txt --output GCF_030035605.1_ASM3003560v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:35,344] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:35,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:35,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:35,360] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:35,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:35,361] [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
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	81.0133	897	1502	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	80.7701	881	1502	95	below_threshold
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	80.4313	808	1502	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.0114	328	1502	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.983	317	1502	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	77.7677	237	1502	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	77.7167	190	1502	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	77.694	258	1502	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	77.5762	124	1502	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	77.4796	217	1502	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	77.4309	229	1502	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	77.2797	160	1502	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.8874	102	1502	95	below_threshold
Aquitalea pelogenes	strain=CCM 7557	GCA_001515305.1	1293573	1293573	type	True	76.8199	169	1502	95	below_threshold
Chromobacterium haemolyticum	strain=DSM 19808	GCA_000711885.1	394935	394935	type	True	76.6506	129	1502	95	below_threshold
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	76.4327	96	1502	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.2747	98	1502	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	76.0163	91	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:35,362] [INFO] DFAST Taxonomy check result was written to GCF_030035605.1_ASM3003560v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:35,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:35,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:35,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference/checkm_data
[2024-01-24 13:22:35,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:35,409] [INFO] Task started: CheckM
[2024-01-24 13:22:35,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030035605.1_ASM3003560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030035605.1_ASM3003560v1_genomic.fna/checkm_input GCF_030035605.1_ASM3003560v1_genomic.fna/checkm_result
[2024-01-24 13:23:24,088] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:24,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,108] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:24,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:24,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030035605.1_ASM3003560v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:24,109] [INFO] Task started: Blastn
[2024-01-24 13:23:24,109] [INFO] Running command: blastn -query GCF_030035605.1_ASM3003560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c3f41ab-119c-4b08-bdcf-2cf0fd215a0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030035605.1_ASM3003560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:25,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:25,419] [INFO] Selected 13 target genomes.
[2024-01-24 13:23:25,419] [INFO] Target genome list was writen to GCF_030035605.1_ASM3003560v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:25,444] [INFO] Task started: fastANI
[2024-01-24 13:23:25,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg61eedc52-3e00-4727-9a55-17e5655151fd/GCF_030035605.1_ASM3003560v1_genomic.fna.gz --refList GCF_030035605.1_ASM3003560v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030035605.1_ASM3003560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:35,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:35,740] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:23:35,740] [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_014645535.1	s__Silvimonas iriomotensis	81.0082	898	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202765.1	s__Silvimonas terrae	80.7675	881	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645555.1	s__Silvimonas amylolytica	80.4269	809	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001313065.1	s__Amantichitinum sp001313065	79.524	484	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294205.1	s__Amantichitinum ursilacus	79.3875	601	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	77.986	316	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	77.9149	305	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	77.7677	237	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048205.1	s__Chitiniphilus eburneus	77.5216	291	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	77.4661	218	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391415.1	s__Aquitalea sp013391415	77.0657	158	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003052555.1	s__Chromobacterium sp003052555	76.9259	154	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001515305.1	s__Aquitalea pelogenes	76.8341	168	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	97.38	96.32	0.89	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:35,742] [INFO] GTDB search result was written to GCF_030035605.1_ASM3003560v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:35,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:35,747] [INFO] DFAST_QC result json was written to GCF_030035605.1_ASM3003560v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:35,747] [INFO] DFAST_QC completed!
[2024-01-24 13:23:35,747] [INFO] Total running time: 0h1m35s