[2024-01-24 11:12:28,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference
[2024-01-24 11:12:29,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,410] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c0f9127-bd61-4a83-8c06-1f206109971e/GCF_025821915.1_ASM2582191v1_genomic.fna.gz | prodigal -d GCF_025821915.1_ASM2582191v1_genomic.fna/cds.fna -a GCF_025821915.1_ASM2582191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:45,537] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:45,537] [INFO] Task started: HMMsearch
[2024-01-24 11:12:45,537] [INFO] Running command: hmmsearch --tblout GCF_025821915.1_ASM2582191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference/reference_markers.hmm GCF_025821915.1_ASM2582191v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:45,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:45,842] [INFO] Found 6/6 markers.
[2024-01-24 11:12:45,894] [INFO] Query marker FASTA was written to GCF_025821915.1_ASM2582191v1_genomic.fna/markers.fasta
[2024-01-24 11:12:45,895] [INFO] Task started: Blastn
[2024-01-24 11:12:45,895] [INFO] Running command: blastn -query GCF_025821915.1_ASM2582191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference/reference_markers.fasta -out GCF_025821915.1_ASM2582191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:47,079] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:47,083] [INFO] Selected 17 target genomes.
[2024-01-24 11:12:47,083] [INFO] Target genome list was writen to GCF_025821915.1_ASM2582191v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:47,090] [INFO] Task started: fastANI
[2024-01-24 11:12:47,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c0f9127-bd61-4a83-8c06-1f206109971e/GCF_025821915.1_ASM2582191v1_genomic.fna.gz --refList GCF_025821915.1_ASM2582191v1_genomic.fna/target_genomes.txt --output GCF_025821915.1_ASM2582191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:09,290] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:09,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:09,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:09,305] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:09,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:09,306] [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 bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	99.9801	1701	1726	95	conclusive
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	99.7851	1659	1726	95	conclusive
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	84.1503	1328	1726	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	84.118	1150	1726	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.0824	1176	1726	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	84.0534	1252	1726	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	84.0269	1286	1726	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	83.7535	1076	1726	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	83.7145	1183	1726	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	83.7064	1177	1726	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.5994	1255	1726	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.3055	1216	1726	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	83.2984	1237	1726	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	83.1748	1150	1726	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.1539	1154	1726	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	81.7203	1122	1726	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.7924	976	1726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:09,308] [INFO] DFAST Taxonomy check result was written to GCF_025821915.1_ASM2582191v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:09,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:09,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:09,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference/checkm_data
[2024-01-24 11:13:09,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:09,365] [INFO] Task started: CheckM
[2024-01-24 11:13:09,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821915.1_ASM2582191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821915.1_ASM2582191v1_genomic.fna/checkm_input GCF_025821915.1_ASM2582191v1_genomic.fna/checkm_result
[2024-01-24 11:13:57,298] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:57,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:57,320] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:57,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:57,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821915.1_ASM2582191v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:57,322] [INFO] Task started: Blastn
[2024-01-24 11:13:57,322] [INFO] Running command: blastn -query GCF_025821915.1_ASM2582191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445e5061-9942-41a3-b69b-05e25d4f4e1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821915.1_ASM2582191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:59,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:59,032] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:59,032] [INFO] Target genome list was writen to GCF_025821915.1_ASM2582191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:59,046] [INFO] Task started: fastANI
[2024-01-24 11:13:59,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c0f9127-bd61-4a83-8c06-1f206109971e/GCF_025821915.1_ASM2582191v1_genomic.fna.gz --refList GCF_025821915.1_ASM2582191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821915.1_ASM2582191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:23,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:23,304] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:23,304] [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_001053185.1	s__Mycobacterium bohemicum	99.7851	1659	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	conclusive
GCF_902652685.1	s__Mycobacterium sp902652685	84.5524	1321	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	84.1398	1330	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001668725.1	s__Mycobacterium sp001668725	84.072	1314	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	84.0255	1245	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	84.0224	1286	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900157385.1	s__Mycobacterium terramassiliense	83.993	1333	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.9883	1321	1726	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	83.9286	1273	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	83.9046	1326	1726	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	83.7616	1257	1726	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	83.7016	1184	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455205.1	s__Mycobacterium sp000455205	83.6332	1246	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_001672815.1	s__Mycobacterium sp001672815	83.5971	1224	1726	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	83.5837	1232	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_001665605.1	s__Mycobacterium sp001665605	83.2647	1236	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	-
GCF_001667075.1	s__Mycobacterium sp001667075	83.1831	1216	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_001953985.1	s__Mycobacterium colombiense_B	82.9589	1170	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:23,306] [INFO] GTDB search result was written to GCF_025821915.1_ASM2582191v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:23,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:23,311] [INFO] DFAST_QC result json was written to GCF_025821915.1_ASM2582191v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:23,311] [INFO] DFAST_QC completed!
[2024-01-24 11:14:23,311] [INFO] Total running time: 0h1m55s