[2024-01-25 18:47:50,897] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:50,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:50,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference
[2024-01-25 18:47:52,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:52,023] [INFO] Task started: Prodigal
[2024-01-25 18:47:52,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7e58360-140e-4ac1-a480-fb6e2a7f875a/GCF_002086775.1_ASM208677v1_genomic.fna.gz | prodigal -d GCF_002086775.1_ASM208677v1_genomic.fna/cds.fna -a GCF_002086775.1_ASM208677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:06,963] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:06,963] [INFO] Task started: HMMsearch
[2024-01-25 18:48:06,963] [INFO] Running command: hmmsearch --tblout GCF_002086775.1_ASM208677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference/reference_markers.hmm GCF_002086775.1_ASM208677v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:07,242] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:07,243] [INFO] Found 6/6 markers.
[2024-01-25 18:48:07,295] [INFO] Query marker FASTA was written to GCF_002086775.1_ASM208677v1_genomic.fna/markers.fasta
[2024-01-25 18:48:07,295] [INFO] Task started: Blastn
[2024-01-25 18:48:07,295] [INFO] Running command: blastn -query GCF_002086775.1_ASM208677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference/reference_markers.fasta -out GCF_002086775.1_ASM208677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:08,487] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:08,489] [INFO] Selected 26 target genomes.
[2024-01-25 18:48:08,489] [INFO] Target genome list was writen to GCF_002086775.1_ASM208677v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:08,500] [INFO] Task started: fastANI
[2024-01-25 18:48:08,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7e58360-140e-4ac1-a480-fb6e2a7f875a/GCF_002086775.1_ASM208677v1_genomic.fna.gz --refList GCF_002086775.1_ASM208677v1_genomic.fna/target_genomes.txt --output GCF_002086775.1_ASM208677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:41,062] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:41,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:41,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:41,077] [INFO] Found 26 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:48:41,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:41,078] [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
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	98.8261	1460	1654	95	conclusive
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	98.7138	1359	1654	95	conclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.4446	1376	1654	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.4416	1375	1654	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	87.353	1337	1654	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	87.3178	1383	1654	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	87.2993	1385	1654	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	87.2779	1245	1654	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	87.0368	1334	1654	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	86.9821	1328	1654	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	86.98	1377	1654	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	86.9703	1372	1654	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	86.5788	1364	1654	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.5669	1389	1654	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	86.2257	1269	1654	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.6416	1212	1654	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	80.8514	935	1654	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	80.6262	890	1654	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	80.6137	868	1654	95	below_threshold
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	80.5415	881	1654	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.4131	740	1654	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	80.3932	846	1654	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.3799	751	1654	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.1713	809	1654	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	79.583	765	1654	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	79.3368	772	1654	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:41,079] [INFO] DFAST Taxonomy check result was written to GCF_002086775.1_ASM208677v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:41,079] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:41,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:41,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference/checkm_data
[2024-01-25 18:48:41,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:41,140] [INFO] Task started: CheckM
[2024-01-25 18:48:41,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086775.1_ASM208677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086775.1_ASM208677v1_genomic.fna/checkm_input GCF_002086775.1_ASM208677v1_genomic.fna/checkm_result
[2024-01-25 18:49:30,122] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:30,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:30,142] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:30,142] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:30,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086775.1_ASM208677v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:30,143] [INFO] Task started: Blastn
[2024-01-25 18:49:30,143] [INFO] Running command: blastn -query GCF_002086775.1_ASM208677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1edf2d2e-c72c-4b95-8890-bfad27d070bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086775.1_ASM208677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:31,951] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:31,953] [INFO] Selected 29 target genomes.
[2024-01-25 18:49:31,954] [INFO] Target genome list was writen to GCF_002086775.1_ASM208677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:31,982] [INFO] Task started: fastANI
[2024-01-25 18:49:31,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7e58360-140e-4ac1-a480-fb6e2a7f875a/GCF_002086775.1_ASM208677v1_genomic.fna.gz --refList GCF_002086775.1_ASM208677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086775.1_ASM208677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:08,731] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:08,749] [INFO] Found 29 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 18:50:08,749] [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_009741445.1	s__Mycobacterium avium	98.807	1462	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	inconclusive
GCA_002291465.1	s__Mycobacterium lepraemurium	96.9338	1242	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000277125.1	s__Mycobacterium intracellulare	87.4303	1376	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_010731675.1	s__Mycobacterium marseillense	87.0428	1333	1654	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	86.989	1275	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	86.976	1377	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001665835.1	s__Mycobacterium colombiense_A	86.8989	1321	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672755.1	s__Mycobacterium colombiense_C	86.8686	1321	1654	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	86.8119	1259	1654	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	86.7752	1291	1654	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	86.6517	1233	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_010731775.1	s__Mycobacterium mantenii	86.5672	1389	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_001667145.1	s__Mycobacterium sp001667145	85.7465	1272	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	84.7373	1271	1654	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	84.5352	1241	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001667735.1	s__Mycobacterium sp001667735	84.3727	1211	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	84.2559	1202	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.9607	1189	1654	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	83.9176	1165	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730575.1	s__Mycobacterium parmense	83.6186	1216	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	81.9705	978	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002102185.1	s__Mycobacterium fragae	80.8628	933	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592155.1	s__Mycobacterium heckeshornense	80.4003	845	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_008370645.1	s__Mycobacterium simiae_A	80.3705	711	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008709575.1	s__Mycobacterium sp008709575	80.2463	699	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592005.1	s__Mycobacterium palauense	80.0528	822	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347205.1	s__Mycobacterium moriokaense_B	79.8077	812	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	79.6074	764	1654	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_003284965.1	s__Mycobacterium sp003284965	79.3492	716	1654	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 18:50:08,751] [INFO] GTDB search result was written to GCF_002086775.1_ASM208677v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:08,751] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:08,755] [INFO] DFAST_QC result json was written to GCF_002086775.1_ASM208677v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:08,756] [INFO] DFAST_QC completed!
[2024-01-25 18:50:08,756] [INFO] Total running time: 0h2m18s