[2024-01-25 17:41:35,616] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference
[2024-01-25 17:41:36,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,812] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg08c28182-6131-43ef-a85c-e0a60c9ebb92/GCF_002219285.1_ASM221928v1_genomic.fna.gz | prodigal -d GCF_002219285.1_ASM221928v1_genomic.fna/cds.fna -a GCF_002219285.1_ASM221928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:09,251] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:09,251] [INFO] Task started: HMMsearch
[2024-01-25 17:42:09,252] [INFO] Running command: hmmsearch --tblout GCF_002219285.1_ASM221928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference/reference_markers.hmm GCF_002219285.1_ASM221928v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:09,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:09,510] [INFO] Found 6/6 markers.
[2024-01-25 17:42:09,561] [INFO] Query marker FASTA was written to GCF_002219285.1_ASM221928v1_genomic.fna/markers.fasta
[2024-01-25 17:42:09,561] [INFO] Task started: Blastn
[2024-01-25 17:42:09,561] [INFO] Running command: blastn -query GCF_002219285.1_ASM221928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference/reference_markers.fasta -out GCF_002219285.1_ASM221928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:10,745] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:10,748] [INFO] Selected 11 target genomes.
[2024-01-25 17:42:10,749] [INFO] Target genome list was writen to GCF_002219285.1_ASM221928v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:10,759] [INFO] Task started: fastANI
[2024-01-25 17:42:10,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg08c28182-6131-43ef-a85c-e0a60c9ebb92/GCF_002219285.1_ASM221928v1_genomic.fna.gz --refList GCF_002219285.1_ASM221928v1_genomic.fna/target_genomes.txt --output GCF_002219285.1_ASM221928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:27,103] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:27,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:27,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:27,111] [INFO] Found 11 fastANI hits (9 hits with ANI > threshold)
[2024-01-25 17:42:27,111] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:42:27,111] [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 intracellulare subsp. chimaera	strain=DSM 44623	GCA_002219285.1	222805	1767	type	True	100.0	2031	2043	95	inconclusive
Mycobacterium intracellulare subsp. chimaera	strain=JCM_14737	GCA_001938095.1	222805	1767	type	True	99.9992	2034	2043	95	inconclusive
Mycobacterium intracellulare subsp. chimaera	strain=DSM 44623	GCA_002101575.1	222805	1767	type	True	99.9548	1946	2043	95	inconclusive
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	97.806	1718	2043	95	inconclusive
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	97.6345	1650	2043	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	97.6134	1632	2043	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	97.5969	1638	2043	95	inconclusive
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	97.5908	1644	2043	95	inconclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	97.4035	1436	2043	95	inconclusive
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	92.26	1618	2043	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.0276	1181	2043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:27,113] [INFO] DFAST Taxonomy check result was written to GCF_002219285.1_ASM221928v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:27,113] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:27,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:27,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference/checkm_data
[2024-01-25 17:42:27,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:27,170] [INFO] Task started: CheckM
[2024-01-25 17:42:27,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002219285.1_ASM221928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002219285.1_ASM221928v1_genomic.fna/checkm_input GCF_002219285.1_ASM221928v1_genomic.fna/checkm_result
[2024-01-25 17:44:06,334] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:06,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:06,359] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:06,359] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:06,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002219285.1_ASM221928v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:06,362] [INFO] Task started: Blastn
[2024-01-25 17:44:06,362] [INFO] Running command: blastn -query GCF_002219285.1_ASM221928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ba8a21-984e-4bfa-80f4-6265579fefb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002219285.1_ASM221928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:08,137] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:08,140] [INFO] Selected 17 target genomes.
[2024-01-25 17:44:08,140] [INFO] Target genome list was writen to GCF_002219285.1_ASM221928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:08,175] [INFO] Task started: fastANI
[2024-01-25 17:44:08,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg08c28182-6131-43ef-a85c-e0a60c9ebb92/GCF_002219285.1_ASM221928v1_genomic.fna.gz --refList GCF_002219285.1_ASM221928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002219285.1_ASM221928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:33,598] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:33,609] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:33,609] [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_000277125.1	s__Mycobacterium intracellulare	97.5969	1638	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	conclusive
GCF_010731675.1	s__Mycobacterium marseillense	92.2691	1617	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_001667315.1	s__Mycobacterium sp001667315	90.6948	1503	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298145.1	s__Mycobacterium sp004298145	89.8448	1442	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665835.1	s__Mycobacterium colombiense_A	87.2884	1455	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104765.1	s__Mycobacterium vulneris	87.1761	1434	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	87.0667	1399	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284975.1	s__Mycobacterium europaeum_A	86.9931	1370	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001665875.1	s__Mycobacterium sp001665875	86.8548	1411	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	84.436	1307	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_001907675.1	s__Mycobacterium paraffinicum	84.4304	1371	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	84.0782	1313	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_002101815.1	s__Mycobacterium paraense	83.9002	1297	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667015.1	s__Mycobacterium sp001667015	83.7401	1232	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	83.7119	1223	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	83.5914	1263	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101785.1	s__Mycobacterium palustre	83.5182	1203	2043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:33,611] [INFO] GTDB search result was written to GCF_002219285.1_ASM221928v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:33,612] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:33,617] [INFO] DFAST_QC result json was written to GCF_002219285.1_ASM221928v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:33,617] [INFO] DFAST_QC completed!
[2024-01-25 17:44:33,617] [INFO] Total running time: 0h2m58s