[2024-01-24 13:41:10,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference
[2024-01-24 13:41:11,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,727] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg94783ea8-09b0-4306-bd9e-9dae40f23b18/GCF_014201505.1_ASM1420150v1_genomic.fna.gz | prodigal -d GCF_014201505.1_ASM1420150v1_genomic.fna/cds.fna -a GCF_014201505.1_ASM1420150v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:22,950] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:22,951] [INFO] Task started: HMMsearch
[2024-01-24 13:41:22,951] [INFO] Running command: hmmsearch --tblout GCF_014201505.1_ASM1420150v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference/reference_markers.hmm GCF_014201505.1_ASM1420150v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:23,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:23,255] [INFO] Found 6/6 markers.
[2024-01-24 13:41:23,288] [INFO] Query marker FASTA was written to GCF_014201505.1_ASM1420150v1_genomic.fna/markers.fasta
[2024-01-24 13:41:23,288] [INFO] Task started: Blastn
[2024-01-24 13:41:23,289] [INFO] Running command: blastn -query GCF_014201505.1_ASM1420150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference/reference_markers.fasta -out GCF_014201505.1_ASM1420150v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:23,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:23,985] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:23,985] [INFO] Target genome list was writen to GCF_014201505.1_ASM1420150v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:23,993] [INFO] Task started: fastANI
[2024-01-24 13:41:23,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg94783ea8-09b0-4306-bd9e-9dae40f23b18/GCF_014201505.1_ASM1420150v1_genomic.fna.gz --refList GCF_014201505.1_ASM1420150v1_genomic.fna/target_genomes.txt --output GCF_014201505.1_ASM1420150v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:39,336] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:39,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:39,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:39,345] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:39,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:39,346] [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
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	100.0	1231	1233	95	conclusive
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	99.9784	1198	1233	95	conclusive
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.6956	194	1233	95	below_threshold
Desulfofustis glycolicus	strain=DSM 9705	GCA_900130015.1	51195	51195	type	True	77.3925	202	1233	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	77.2593	161	1233	95	below_threshold
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	76.8637	109	1233	95	below_threshold
Desulfosediminicola ganghwensis	strain=IMCC35004	GCA_005116675.2	2569540	2569540	type	True	76.4805	61	1233	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.7232	64	1233	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	74.8483	71	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:39,347] [INFO] DFAST Taxonomy check result was written to GCF_014201505.1_ASM1420150v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:39,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:39,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:39,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference/checkm_data
[2024-01-24 13:41:39,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:39,393] [INFO] Task started: CheckM
[2024-01-24 13:41:39,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201505.1_ASM1420150v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201505.1_ASM1420150v1_genomic.fna/checkm_input GCF_014201505.1_ASM1420150v1_genomic.fna/checkm_result
[2024-01-24 13:42:15,570] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,590] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201505.1_ASM1420150v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,591] [INFO] Task started: Blastn
[2024-01-24 13:42:15,592] [INFO] Running command: blastn -query GCF_014201505.1_ASM1420150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45b74e37-e080-4d52-8580-6c9ee2e42bb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201505.1_ASM1420150v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,480] [INFO] Selected 21 target genomes.
[2024-01-24 13:42:16,481] [INFO] Target genome list was writen to GCF_014201505.1_ASM1420150v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,517] [INFO] Task started: fastANI
[2024-01-24 13:42:16,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg94783ea8-09b0-4306-bd9e-9dae40f23b18/GCF_014201505.1_ASM1420150v1_genomic.fna.gz --refList GCF_014201505.1_ASM1420150v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201505.1_ASM1420150v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:29,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:29,810] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:29,810] [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_014201505.1	s__Desulfoprunum benzoelyticum	100.0	1231	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_000769715.1	s__Desulfoprunum sp000769715	88.5838	903	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.79	99.74	0.93	0.93	5	-
GCA_008933635.1	s__Desulfoprunum sp008933635	81.32	622	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961725.1	s__Desulforhopalus sp000961725	78.4531	208	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390165.1	s__Desulforhopalus sp011390165	77.3634	192	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875445.1	s__Desulforhopalus sp903875445	77.1587	159	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	99.93	99.88	0.93	0.87	5	-
GCA_001799365.1	s__Desulforhopalus sp001799365	77.1122	226	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013426795.1	s__UBA2270 sp013426795	76.8384	93	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116645.1	s__Desulforhopalus sp005116645	76.7939	113	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773475.1	s__UBA2270 sp009773475	76.5757	60	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903869265.1	s__UBA2262 sp903869265	76.5619	69	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	100.00	99.97	1.00	1.00	39	-
GCA_002347095.1	s__UBA2262 sp002347095	76.533	75	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	98.22	98.22	0.94	0.94	2	-
GCA_018821985.1	s__UBA2270 sp018821985	76.1086	65	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	99.96	99.93	0.98	0.98	3	-
GCA_002347185.1	s__UBA2262 sp002347185	76.0511	89	1233	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	99.47	99.47	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,811] [INFO] GTDB search result was written to GCF_014201505.1_ASM1420150v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:29,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:29,815] [INFO] DFAST_QC result json was written to GCF_014201505.1_ASM1420150v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:29,815] [INFO] DFAST_QC completed!
[2024-01-24 13:42:29,815] [INFO] Total running time: 0h1m19s