[2024-01-25 18:53:05,727] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,729] [INFO] DQC Reference Directory: /var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference
[2024-01-25 18:53:06,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:06,900] [INFO] Task started: Prodigal
[2024-01-25 18:53:06,900] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf6d51d4-1724-4bbd-a6f6-e4ac3b0af711/GCF_025822265.1_ASM2582226v1_genomic.fna.gz | prodigal -d GCF_025822265.1_ASM2582226v1_genomic.fna/cds.fna -a GCF_025822265.1_ASM2582226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:28,583] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:28,583] [INFO] Task started: HMMsearch
[2024-01-25 18:53:28,583] [INFO] Running command: hmmsearch --tblout GCF_025822265.1_ASM2582226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference/reference_markers.hmm GCF_025822265.1_ASM2582226v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:28,943] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:28,944] [INFO] Found 6/6 markers.
[2024-01-25 18:53:29,005] [INFO] Query marker FASTA was written to GCF_025822265.1_ASM2582226v1_genomic.fna/markers.fasta
[2024-01-25 18:53:29,005] [INFO] Task started: Blastn
[2024-01-25 18:53:29,005] [INFO] Running command: blastn -query GCF_025822265.1_ASM2582226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference/reference_markers.fasta -out GCF_025822265.1_ASM2582226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:30,201] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:30,204] [INFO] Selected 20 target genomes.
[2024-01-25 18:53:30,204] [INFO] Target genome list was writen to GCF_025822265.1_ASM2582226v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:30,214] [INFO] Task started: fastANI
[2024-01-25 18:53:30,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf6d51d4-1724-4bbd-a6f6-e4ac3b0af711/GCF_025822265.1_ASM2582226v1_genomic.fna.gz --refList GCF_025822265.1_ASM2582226v1_genomic.fna/target_genomes.txt --output GCF_025822265.1_ASM2582226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:59,031] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:59,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:59,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:59,043] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:53:59,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:53:59,043] [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
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	91.0944	2009	2428	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	91.0131	1958	2428	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	82.6661	1562	2428	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	82.6456	1585	2428	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	81.9796	1301	2428	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	81.9738	1305	2428	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	81.8641	1259	2428	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	81.7777	1228	2428	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	81.7432	1124	2428	95	below_threshold
Mycolicibacterium wolinskyi	strain=ATCC 700010	GCA_002101965.1	59750	59750	type	True	81.6624	1361	2428	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	81.6213	1253	2428	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	81.5843	1193	2428	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	81.568	1250	2428	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	81.5062	1153	2428	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	81.3887	1100	2428	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.1199	916	2428	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	79.6105	739	2428	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.468	854	2428	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4185	857	2428	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3301	838	2428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:59,045] [INFO] DFAST Taxonomy check result was written to GCF_025822265.1_ASM2582226v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:59,045] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:59,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:59,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference/checkm_data
[2024-01-25 18:53:59,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:59,113] [INFO] Task started: CheckM
[2024-01-25 18:53:59,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822265.1_ASM2582226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822265.1_ASM2582226v1_genomic.fna/checkm_input GCF_025822265.1_ASM2582226v1_genomic.fna/checkm_result
[2024-01-25 18:55:24,065] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:24,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:24,093] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:24,094] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:24,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822265.1_ASM2582226v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:24,095] [INFO] Task started: Blastn
[2024-01-25 18:55:24,095] [INFO] Running command: blastn -query GCF_025822265.1_ASM2582226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga17cf607-fc6d-47ac-8135-ed2e34d6580a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822265.1_ASM2582226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:26,052] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:26,055] [INFO] Selected 13 target genomes.
[2024-01-25 18:55:26,056] [INFO] Target genome list was writen to GCF_025822265.1_ASM2582226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:26,063] [INFO] Task started: fastANI
[2024-01-25 18:55:26,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf6d51d4-1724-4bbd-a6f6-e4ac3b0af711/GCF_025822265.1_ASM2582226v1_genomic.fna.gz --refList GCF_025822265.1_ASM2582226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822265.1_ASM2582226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:47,249] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:47,258] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:47,258] [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_001570425.1	s__Mycobacterium brisbanense	99.9955	2415	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.59	97.59	0.86	0.86	2	conclusive
GCF_001665685.1	s__Mycobacterium sp001665685	92.285	2033	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086485.1	s__Mycobacterium aquaticum	91.0944	2009	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	91.0081	1959	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382405.1	s__Mycobacterium sp000382405	85.6101	1196	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373905.1	s__Mycobacterium sp000373905	85.5705	1176	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	82.6852	1559	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_900078665.2	s__Mycobacterium houstonense	81.8792	1256	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942045.1	s__Mycobacterium porcinum_A	81.8602	1225	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	81.7964	1336	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	81.7623	1121	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762045.1	s__Mycobacterium sp004762045	81.6578	1292	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101965.1	s__Mycobacterium wolinskyi	81.6506	1363	2428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.70	97.70	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:47,260] [INFO] GTDB search result was written to GCF_025822265.1_ASM2582226v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:47,262] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:47,265] [INFO] DFAST_QC result json was written to GCF_025822265.1_ASM2582226v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:47,265] [INFO] DFAST_QC completed!
[2024-01-25 18:55:47,265] [INFO] Total running time: 0h2m42s