[2023-06-28 01:45:57,611] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:45:57,614] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:45:57,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference
[2023-06-28 01:45:59,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:45:59,050] [INFO] Task started: Prodigal
[2023-06-28 01:45:59,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg734f6043-ebab-4a65-a48e-a89b35fbb28c/GCA_019411245.1_ASM1941124v1_genomic.fna.gz | prodigal -d GCA_019411245.1_ASM1941124v1_genomic.fna/cds.fna -a GCA_019411245.1_ASM1941124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:46:21,561] [INFO] Task succeeded: Prodigal
[2023-06-28 01:46:21,562] [INFO] Task started: HMMsearch
[2023-06-28 01:46:21,562] [INFO] Running command: hmmsearch --tblout GCA_019411245.1_ASM1941124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference/reference_markers.hmm GCA_019411245.1_ASM1941124v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:46:21,857] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:46:21,858] [INFO] Found 6/6 markers.
[2023-06-28 01:46:21,901] [INFO] Query marker FASTA was written to GCA_019411245.1_ASM1941124v1_genomic.fna/markers.fasta
[2023-06-28 01:46:21,902] [INFO] Task started: Blastn
[2023-06-28 01:46:21,902] [INFO] Running command: blastn -query GCA_019411245.1_ASM1941124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference/reference_markers.fasta -out GCA_019411245.1_ASM1941124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:22,527] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:22,531] [INFO] Selected 11 target genomes.
[2023-06-28 01:46:22,531] [INFO] Target genome list was writen to GCA_019411245.1_ASM1941124v1_genomic.fna/target_genomes.txt
[2023-06-28 01:46:22,534] [INFO] Task started: fastANI
[2023-06-28 01:46:22,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg734f6043-ebab-4a65-a48e-a89b35fbb28c/GCA_019411245.1_ASM1941124v1_genomic.fna.gz --refList GCA_019411245.1_ASM1941124v1_genomic.fna/target_genomes.txt --output GCA_019411245.1_ASM1941124v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:46:32,061] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:32,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:46:32,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:46:32,078] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-28 01:46:32,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 01:46:32,078] [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
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	96.6637	1159	1444	95	conclusive
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	96.5947	1160	1444	95	conclusive
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	96.5935	1152	1444	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.5281	302	1444	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	78.3578	330	1444	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	78.1891	300	1444	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	78.1774	301	1444	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	78.1507	307	1444	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	78.1036	317	1444	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:46:32,081] [INFO] DFAST Taxonomy check result was written to GCA_019411245.1_ASM1941124v1_genomic.fna/tc_result.tsv
[2023-06-28 01:46:32,082] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:46:32,082] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:46:32,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference/checkm_data
[2023-06-28 01:46:32,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:46:32,127] [INFO] Task started: CheckM
[2023-06-28 01:46:32,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019411245.1_ASM1941124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019411245.1_ASM1941124v1_genomic.fna/checkm_input GCA_019411245.1_ASM1941124v1_genomic.fna/checkm_result
[2023-06-28 01:47:32,605] [INFO] Task succeeded: CheckM
[2023-06-28 01:47:32,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:47:32,631] [INFO] ===== Completeness check finished =====
[2023-06-28 01:47:32,631] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:47:32,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019411245.1_ASM1941124v1_genomic.fna/markers.fasta)
[2023-06-28 01:47:32,632] [INFO] Task started: Blastn
[2023-06-28 01:47:32,632] [INFO] Running command: blastn -query GCA_019411245.1_ASM1941124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d42bbcb-acf0-4d7c-9931-aa8adb08b5c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_019411245.1_ASM1941124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:47:33,422] [INFO] Task succeeded: Blastn
[2023-06-28 01:47:33,426] [INFO] Selected 15 target genomes.
[2023-06-28 01:47:33,426] [INFO] Target genome list was writen to GCA_019411245.1_ASM1941124v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:47:33,437] [INFO] Task started: fastANI
[2023-06-28 01:47:33,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg734f6043-ebab-4a65-a48e-a89b35fbb28c/GCA_019411245.1_ASM1941124v1_genomic.fna.gz --refList GCA_019411245.1_ASM1941124v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019411245.1_ASM1941124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:47:45,795] [INFO] Task succeeded: fastANI
[2023-06-28 01:47:45,812] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:47:45,812] [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_000012845.1	s__Parabacteroides distasonis	96.5947	1160	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	conclusive
GCF_004793765.1	s__Parabacteroides distasonis_A	94.282	976	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_011038785.1	s__Parabacteroides sp011038785	89.9771	767	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154105.1	s__Parabacteroides merdae	78.5522	304	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_000969835.1	s__Parabacteroides goldsteinii	78.3578	330	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_003363715.1	s__Parabacteroides acidifaciens	78.1681	300	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCF_003480915.1	s__Parabacteroides sp003480915	78.1035	331	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.39	97.67	0.93	0.87	5	-
GCF_000156495.1	s__Parabacteroides johnsonii	78.0976	315	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_900770835.1	s__Parabacteroides sp900770835	78.0687	208	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760525.1	s__Parabacteroides sp900760525	78.0336	286	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.9785	311	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	77.6859	278	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552465.1	s__Parabacteroides sp900552465	77.549	265	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	77.202	153	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
GCF_012113595.1	s__Bacteroides sp012113595	76.5049	60	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:47:45,820] [INFO] GTDB search result was written to GCA_019411245.1_ASM1941124v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:47:45,820] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:47:45,824] [INFO] DFAST_QC result json was written to GCA_019411245.1_ASM1941124v1_genomic.fna/dqc_result.json
[2023-06-28 01:47:45,824] [INFO] DFAST_QC completed!
[2023-06-28 01:47:45,824] [INFO] Total running time: 0h1m48s