[2023-06-27 09:01:48,934] [INFO] DFAST_QC pipeline started.
[2023-06-27 09:01:48,937] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 09:01:48,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference
[2023-06-27 09:01:50,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 09:01:50,224] [INFO] Task started: Prodigal
[2023-06-27 09:01:50,224] [INFO] Running command: gunzip -c /var/lib/cwl/stgde10579d-d501-4c58-b5d8-27f9011abed0/GCA_026705605.1_ASM2670560v1_genomic.fna.gz | prodigal -d GCA_026705605.1_ASM2670560v1_genomic.fna/cds.fna -a GCA_026705605.1_ASM2670560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 09:01:57,788] [INFO] Task succeeded: Prodigal
[2023-06-27 09:01:57,788] [INFO] Task started: HMMsearch
[2023-06-27 09:01:57,789] [INFO] Running command: hmmsearch --tblout GCA_026705605.1_ASM2670560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference/reference_markers.hmm GCA_026705605.1_ASM2670560v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 09:01:57,966] [INFO] Task succeeded: HMMsearch
[2023-06-27 09:01:57,967] [INFO] Found 6/6 markers.
[2023-06-27 09:01:58,005] [INFO] Query marker FASTA was written to GCA_026705605.1_ASM2670560v1_genomic.fna/markers.fasta
[2023-06-27 09:01:58,006] [INFO] Task started: Blastn
[2023-06-27 09:01:58,006] [INFO] Running command: blastn -query GCA_026705605.1_ASM2670560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference/reference_markers.fasta -out GCA_026705605.1_ASM2670560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:01:58,656] [INFO] Task succeeded: Blastn
[2023-06-27 09:01:58,660] [INFO] Selected 20 target genomes.
[2023-06-27 09:01:58,660] [INFO] Target genome list was writen to GCA_026705605.1_ASM2670560v1_genomic.fna/target_genomes.txt
[2023-06-27 09:01:58,664] [INFO] Task started: fastANI
[2023-06-27 09:01:58,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgde10579d-d501-4c58-b5d8-27f9011abed0/GCA_026705605.1_ASM2670560v1_genomic.fna.gz --refList GCA_026705605.1_ASM2670560v1_genomic.fna/target_genomes.txt --output GCA_026705605.1_ASM2670560v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 09:02:12,847] [INFO] Task succeeded: fastANI
[2023-06-27 09:02:12,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 09:02:12,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 09:02:12,858] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 09:02:12,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 09:02:12,858] [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
Tepidiforma bonchosmolovskayae	strain=3753O	GCA_008838325.1	2601677	2601677	type	True	77.3811	192	924	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	75.1719	56	924	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	75.021	96	924	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.9611	102	924	95	below_threshold
Geodermatophilus amargosae	strain=DSM 46136	GCA_900116515.1	1296565	1296565	type	True	74.9567	107	924	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	74.8774	99	924	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	74.7633	102	924	95	below_threshold
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	74.6911	56	924	95	below_threshold
Burkholderia latens	strain=CCUG 54555	GCA_008802135.1	488446	488446	suspected-type	True	74.6887	56	924	95	below_threshold
Burkholderia vietnamiensis	strain=FDAARGOS_1488	GCA_020099355.1	60552	60552	type	True	74.6438	65	924	95	below_threshold
Burkholderia vietnamiensis	strain=LMG 10929	GCA_000959445.1	60552	60552	type	True	74.642	64	924	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 09:02:12,860] [INFO] DFAST Taxonomy check result was written to GCA_026705605.1_ASM2670560v1_genomic.fna/tc_result.tsv
[2023-06-27 09:02:12,860] [INFO] ===== Taxonomy check completed =====
[2023-06-27 09:02:12,860] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 09:02:12,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference/checkm_data
[2023-06-27 09:02:12,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 09:02:12,892] [INFO] Task started: CheckM
[2023-06-27 09:02:12,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026705605.1_ASM2670560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026705605.1_ASM2670560v1_genomic.fna/checkm_input GCA_026705605.1_ASM2670560v1_genomic.fna/checkm_result
[2023-06-27 09:02:38,562] [INFO] Task succeeded: CheckM
[2023-06-27 09:02:38,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 09:02:38,587] [INFO] ===== Completeness check finished =====
[2023-06-27 09:02:38,587] [INFO] ===== Start GTDB Search =====
[2023-06-27 09:02:38,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026705605.1_ASM2670560v1_genomic.fna/markers.fasta)
[2023-06-27 09:02:38,587] [INFO] Task started: Blastn
[2023-06-27 09:02:38,587] [INFO] Running command: blastn -query GCA_026705605.1_ASM2670560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg039c190d-a9a1-4d68-b76b-d31938c91076/dqc_reference/reference_markers_gtdb.fasta -out GCA_026705605.1_ASM2670560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:02:39,565] [INFO] Task succeeded: Blastn
[2023-06-27 09:02:39,570] [INFO] Selected 15 target genomes.
[2023-06-27 09:02:39,570] [INFO] Target genome list was writen to GCA_026705605.1_ASM2670560v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 09:02:39,577] [INFO] Task started: fastANI
[2023-06-27 09:02:39,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgde10579d-d501-4c58-b5d8-27f9011abed0/GCA_026705605.1_ASM2670560v1_genomic.fna.gz --refList GCA_026705605.1_ASM2670560v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026705605.1_ASM2670560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 09:02:47,748] [INFO] Task succeeded: fastANI
[2023-06-27 09:02:47,760] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 09:02:47,760] [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
GCA_009838385.1	s__UBA2991 sp009838385	94.291	476	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UBA2991	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841435.1	s__UBA2991 sp009841435	93.5716	754	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UBA2991	95.0	97.17	95.58	0.93	0.85	4	-
GCA_009839725.1	s__UBA2991 sp009839725	87.4406	704	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UBA2991	95.0	97.52	96.30	0.92	0.86	4	-
GCA_016234445.1	s__JACRBT01 sp016234445	77.402	230	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACRBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008838325.1	s__Tepidiforma bonchosmolovskayae	77.352	194	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002563855.1	s__Tepidiforma sp002563855	77.3156	194	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703545.1	s__JACPOQ01 sp016703545	77.2606	215	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577245.1	s__UCB2 sp003577245	77.2431	116	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	99.02	98.75	0.69	0.69	3	-
GCA_011055725.1	s__FeB-14 sp011055725	77.1399	121	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126855.1	s__SLAK01 sp007126855	77.0545	117	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__SLAK01	95.0	98.80	98.80	0.81	0.81	2	-
GCA_015075555.1	s__UCB2 sp015075555	76.9567	150	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003104995.1	s__FeB-14 sp003104995	76.892	168	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	99.84	99.84	0.86	0.86	2	-
GCA_007118095.1	s__SLAK01 sp007118095	76.5349	134	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__SLAK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308185.1	s__PNKC01 sp017308185	76.525	108	924	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__PNKC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 09:02:47,763] [INFO] GTDB search result was written to GCA_026705605.1_ASM2670560v1_genomic.fna/result_gtdb.tsv
[2023-06-27 09:02:47,763] [INFO] ===== GTDB Search completed =====
[2023-06-27 09:02:47,767] [INFO] DFAST_QC result json was written to GCA_026705605.1_ASM2670560v1_genomic.fna/dqc_result.json
[2023-06-27 09:02:47,767] [INFO] DFAST_QC completed!
[2023-06-27 09:02:47,767] [INFO] Total running time: 0h0m59s