[2023-06-28 04:02:14,704] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:02:14,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:02:14,711] [INFO] DQC Reference Directory: /var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference
[2023-06-28 04:02:15,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:02:15,945] [INFO] Task started: Prodigal
[2023-06-28 04:02:15,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77e189a-314b-4cc2-8333-0ae08f4c04c1/GCA_019310245.1_ASM1931024v1_genomic.fna.gz | prodigal -d GCA_019310245.1_ASM1931024v1_genomic.fna/cds.fna -a GCA_019310245.1_ASM1931024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:02:27,423] [INFO] Task succeeded: Prodigal
[2023-06-28 04:02:27,423] [INFO] Task started: HMMsearch
[2023-06-28 04:02:27,423] [INFO] Running command: hmmsearch --tblout GCA_019310245.1_ASM1931024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference/reference_markers.hmm GCA_019310245.1_ASM1931024v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:02:27,680] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:02:27,681] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb77e189a-314b-4cc2-8333-0ae08f4c04c1/GCA_019310245.1_ASM1931024v1_genomic.fna.gz]
[2023-06-28 04:02:27,727] [INFO] Query marker FASTA was written to GCA_019310245.1_ASM1931024v1_genomic.fna/markers.fasta
[2023-06-28 04:02:27,727] [INFO] Task started: Blastn
[2023-06-28 04:02:27,728] [INFO] Running command: blastn -query GCA_019310245.1_ASM1931024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference/reference_markers.fasta -out GCA_019310245.1_ASM1931024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:02:28,297] [INFO] Task succeeded: Blastn
[2023-06-28 04:02:28,300] [INFO] Selected 20 target genomes.
[2023-06-28 04:02:28,300] [INFO] Target genome list was writen to GCA_019310245.1_ASM1931024v1_genomic.fna/target_genomes.txt
[2023-06-28 04:02:28,301] [INFO] Task started: fastANI
[2023-06-28 04:02:28,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77e189a-314b-4cc2-8333-0ae08f4c04c1/GCA_019310245.1_ASM1931024v1_genomic.fna.gz --refList GCA_019310245.1_ASM1931024v1_genomic.fna/target_genomes.txt --output GCA_019310245.1_ASM1931024v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:02:43,711] [INFO] Task succeeded: fastANI
[2023-06-28 04:02:43,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:02:43,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:02:43,723] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:02:43,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:02:43,724] [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
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	75.0035	90	1156	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.9743	100	1156	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.917	95	1156	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.8176	63	1156	95	below_threshold
Micromonospora costi	strain=CS1-12	GCA_003626655.1	1530042	1530042	type	True	74.7123	68	1156	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	74.7098	72	1156	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	74.6799	66	1156	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	74.6329	60	1156	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	74.6041	70	1156	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:02:43,726] [INFO] DFAST Taxonomy check result was written to GCA_019310245.1_ASM1931024v1_genomic.fna/tc_result.tsv
[2023-06-28 04:02:43,726] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:02:43,726] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:02:43,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference/checkm_data
[2023-06-28 04:02:43,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:02:43,770] [INFO] Task started: CheckM
[2023-06-28 04:02:43,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310245.1_ASM1931024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310245.1_ASM1931024v1_genomic.fna/checkm_input GCA_019310245.1_ASM1931024v1_genomic.fna/checkm_result
[2023-06-28 04:03:24,297] [INFO] Task succeeded: CheckM
[2023-06-28 04:03:24,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.24%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:03:24,323] [INFO] ===== Completeness check finished =====
[2023-06-28 04:03:24,324] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:03:24,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310245.1_ASM1931024v1_genomic.fna/markers.fasta)
[2023-06-28 04:03:24,324] [INFO] Task started: Blastn
[2023-06-28 04:03:24,324] [INFO] Running command: blastn -query GCA_019310245.1_ASM1931024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff00ec4-12c4-43a7-b645-7e4e2eb1767f/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310245.1_ASM1931024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:03:24,968] [INFO] Task succeeded: Blastn
[2023-06-28 04:03:24,974] [INFO] Selected 20 target genomes.
[2023-06-28 04:03:24,974] [INFO] Target genome list was writen to GCA_019310245.1_ASM1931024v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:03:24,989] [INFO] Task started: fastANI
[2023-06-28 04:03:24,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77e189a-314b-4cc2-8333-0ae08f4c04c1/GCA_019310245.1_ASM1931024v1_genomic.fna.gz --refList GCA_019310245.1_ASM1931024v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310245.1_ASM1931024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:03:40,024] [INFO] Task succeeded: fastANI
[2023-06-28 04:03:40,040] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:03:40,040] [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_016218815.1	s__JAAZOP01 sp016218815	75.5179	139	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__DRWM01;f__JAAZOP01;g__JAAZOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797735.1	s__JAAZOP01 sp012797735	75.5073	98	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__DRWM01;f__JAAZOP01;g__JAAZOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190375.1	s__JACPQR01 sp016190375	75.2166	128	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__JACPQR01;f__JACPQR01;g__JACPQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	75.0937	123	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_009992505.1	s__JAADHO01 sp009992505	75.0901	69	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	74.9074	158	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCF_003611735.1	s__Corallococcus sicarius	74.9069	97	1156	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	74.8171	106	1156	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900090285.1	s__Micromonospora inositola	74.5984	72	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087345.1	s__Marmoricola_A caldifontis	74.5561	51	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:03:40,042] [INFO] GTDB search result was written to GCA_019310245.1_ASM1931024v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:03:40,043] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:03:40,046] [INFO] DFAST_QC result json was written to GCA_019310245.1_ASM1931024v1_genomic.fna/dqc_result.json
[2023-06-28 04:03:40,046] [INFO] DFAST_QC completed!
[2023-06-28 04:03:40,046] [INFO] Total running time: 0h1m25s