[2024-01-25 19:34:50,987] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:50,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:50,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference
[2024-01-25 19:34:52,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:52,061] [INFO] Task started: Prodigal
[2024-01-25 19:34:52,061] [INFO] Running command: gunzip -c /var/lib/cwl/stga65a455c-6a89-4f22-b0b6-98d8accb1549/GCF_025821415.1_ASM2582141v1_genomic.fna.gz | prodigal -d GCF_025821415.1_ASM2582141v1_genomic.fna/cds.fna -a GCF_025821415.1_ASM2582141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:06,416] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:06,417] [INFO] Task started: HMMsearch
[2024-01-25 19:35:06,417] [INFO] Running command: hmmsearch --tblout GCF_025821415.1_ASM2582141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference/reference_markers.hmm GCF_025821415.1_ASM2582141v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:06,707] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:06,708] [INFO] Found 6/6 markers.
[2024-01-25 19:35:06,756] [INFO] Query marker FASTA was written to GCF_025821415.1_ASM2582141v1_genomic.fna/markers.fasta
[2024-01-25 19:35:06,756] [INFO] Task started: Blastn
[2024-01-25 19:35:06,757] [INFO] Running command: blastn -query GCF_025821415.1_ASM2582141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference/reference_markers.fasta -out GCF_025821415.1_ASM2582141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:07,819] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:07,821] [INFO] Selected 22 target genomes.
[2024-01-25 19:35:07,822] [INFO] Target genome list was writen to GCF_025821415.1_ASM2582141v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:07,830] [INFO] Task started: fastANI
[2024-01-25 19:35:07,830] [INFO] Running command: fastANI --query /var/lib/cwl/stga65a455c-6a89-4f22-b0b6-98d8accb1549/GCF_025821415.1_ASM2582141v1_genomic.fna.gz --refList GCF_025821415.1_ASM2582141v1_genomic.fna/target_genomes.txt --output GCF_025821415.1_ASM2582141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:32,986] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:32,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:32,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:32,999] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:35:32,999] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:35:32,999] [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 paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	91.5562	1410	1737	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	86.1479	1134	1737	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	86.1397	1105	1737	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.3783	1174	1737	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	84.1735	1263	1737	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	84.0106	1211	1737	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	84.0083	1097	1737	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	84.0074	1240	1737	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	83.9827	1141	1737	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	83.7057	1150	1737	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.6947	1154	1737	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	83.6743	1155	1737	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	83.6033	1166	1737	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	83.4293	1159	1737	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	83.3743	1168	1737	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	83.3168	1153	1737	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	83.2486	1190	1737	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	82.2591	947	1737	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	82.2545	927	1737	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	81.288	939	1737	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	81.255	940	1737	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	81.1984	959	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:33,000] [INFO] DFAST Taxonomy check result was written to GCF_025821415.1_ASM2582141v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:33,001] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:33,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:33,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference/checkm_data
[2024-01-25 19:35:33,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:33,075] [INFO] Task started: CheckM
[2024-01-25 19:35:33,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821415.1_ASM2582141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821415.1_ASM2582141v1_genomic.fna/checkm_input GCF_025821415.1_ASM2582141v1_genomic.fna/checkm_result
[2024-01-25 19:36:17,733] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:17,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:17,754] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:17,755] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:17,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821415.1_ASM2582141v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:17,756] [INFO] Task started: Blastn
[2024-01-25 19:36:17,756] [INFO] Running command: blastn -query GCF_025821415.1_ASM2582141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg889fd593-bb47-4025-924c-6112f9aff929/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821415.1_ASM2582141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:19,391] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:19,394] [INFO] Selected 14 target genomes.
[2024-01-25 19:36:19,394] [INFO] Target genome list was writen to GCF_025821415.1_ASM2582141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:19,404] [INFO] Task started: fastANI
[2024-01-25 19:36:19,404] [INFO] Running command: fastANI --query /var/lib/cwl/stga65a455c-6a89-4f22-b0b6-98d8accb1549/GCF_025821415.1_ASM2582141v1_genomic.fna.gz --refList GCF_025821415.1_ASM2582141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821415.1_ASM2582141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:39,215] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:39,227] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:39,228] [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_900078675.2	s__Mycobacterium interjectum	99.7646	1707	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900157385.1	s__Mycobacterium terramassiliense	93.7375	1502	1737	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	93.2671	1482	1737	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	92.2729	1369	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	91.5905	1409	1737	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	91.5658	1409	1737	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	89.1402	1350	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001665295.1	s__Mycobacterium sp001665295	86.9745	1322	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672815.1	s__Mycobacterium sp001672815	86.6364	1289	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	86.1913	1286	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_002101785.1	s__Mycobacterium palustre	85.3623	1175	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954275.1	s__Mycobacterium sp001954275	84.1503	1131	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	84.0349	1209	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	83.4395	1158	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:39,236] [INFO] GTDB search result was written to GCF_025821415.1_ASM2582141v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:39,237] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:39,243] [INFO] DFAST_QC result json was written to GCF_025821415.1_ASM2582141v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:39,243] [INFO] DFAST_QC completed!
[2024-01-25 19:36:39,243] [INFO] Total running time: 0h1m48s