[2024-01-25 18:51:05,825] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference
[2024-01-25 18:51:06,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:06,997] [INFO] Task started: Prodigal
[2024-01-25 18:51:06,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e1196ef-733c-4fa9-87e8-818126eb4149/GCF_002102095.1_ASM210209v1_genomic.fna.gz | prodigal -d GCF_002102095.1_ASM210209v1_genomic.fna/cds.fna -a GCF_002102095.1_ASM210209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:30,308] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:30,309] [INFO] Task started: HMMsearch
[2024-01-25 18:51:30,309] [INFO] Running command: hmmsearch --tblout GCF_002102095.1_ASM210209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference/reference_markers.hmm GCF_002102095.1_ASM210209v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:30,584] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:30,585] [INFO] Found 6/6 markers.
[2024-01-25 18:51:30,633] [INFO] Query marker FASTA was written to GCF_002102095.1_ASM210209v1_genomic.fna/markers.fasta
[2024-01-25 18:51:30,634] [INFO] Task started: Blastn
[2024-01-25 18:51:30,634] [INFO] Running command: blastn -query GCF_002102095.1_ASM210209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference/reference_markers.fasta -out GCF_002102095.1_ASM210209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:31,679] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:31,683] [INFO] Selected 19 target genomes.
[2024-01-25 18:51:31,683] [INFO] Target genome list was writen to GCF_002102095.1_ASM210209v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:31,685] [INFO] Task started: fastANI
[2024-01-25 18:51:31,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e1196ef-733c-4fa9-87e8-818126eb4149/GCF_002102095.1_ASM210209v1_genomic.fna.gz --refList GCF_002102095.1_ASM210209v1_genomic.fna/target_genomes.txt --output GCF_002102095.1_ASM210209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:58,601] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:58,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:58,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:58,614] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:51:58,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:58,614] [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 conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	100.0	2017	2021	95	conclusive
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	99.9916	2018	2021	95	conclusive
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.818	1152	2021	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	83.7398	1126	2021	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	83.0702	1300	2021	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	82.8518	1183	2021	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	82.7786	1101	2021	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	82.7623	1170	2021	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	82.4033	1155	2021	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	82.3739	1177	2021	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	82.3418	1194	2021	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	82.3079	1046	2021	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	82.2865	1173	2021	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	82.2308	1139	2021	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	81.9865	1022	2021	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	81.9003	1048	2021	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	81.8096	902	2021	95	below_threshold
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	80.9446	1149	2021	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	80.8803	1164	2021	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:58,616] [INFO] DFAST Taxonomy check result was written to GCF_002102095.1_ASM210209v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:58,616] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:58,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:58,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference/checkm_data
[2024-01-25 18:51:58,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:58,677] [INFO] Task started: CheckM
[2024-01-25 18:51:58,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102095.1_ASM210209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102095.1_ASM210209v1_genomic.fna/checkm_input GCF_002102095.1_ASM210209v1_genomic.fna/checkm_result
[2024-01-25 18:53:07,641] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:07,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:07,672] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:07,672] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:07,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102095.1_ASM210209v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:07,673] [INFO] Task started: Blastn
[2024-01-25 18:53:07,673] [INFO] Running command: blastn -query GCF_002102095.1_ASM210209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2cd6c42-5156-4b81-b8a6-73f3ea6ba7c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102095.1_ASM210209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:09,206] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:09,208] [INFO] Selected 23 target genomes.
[2024-01-25 18:53:09,209] [INFO] Target genome list was writen to GCF_002102095.1_ASM210209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:09,223] [INFO] Task started: fastANI
[2024-01-25 18:53:09,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e1196ef-733c-4fa9-87e8-818126eb4149/GCF_002102095.1_ASM210209v1_genomic.fna.gz --refList GCF_002102095.1_ASM210209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102095.1_ASM210209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:42,002] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:42,015] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:42,016] [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_010730195.1	s__Mycobacterium conspicuum	99.9916	2018	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_010730745.1	s__Mycobacterium heidelbergense	83.8128	1152	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.1691	1254	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086305.1	s__Mycobacterium malmoense_B	83.066	1130	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_002086635.1	s__Mycobacterium alsense	83.0021	1236	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001667185.1	s__Mycobacterium sp001667185	82.9172	1235	2021	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	82.8649	1184	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	82.8596	1303	2021	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	82.8065	1293	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741445.1	s__Mycobacterium avium	82.7674	1170	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_001954275.1	s__Mycobacterium sp001954275	82.6994	1163	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	82.3994	1219	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_007714205.1	s__Mycobacterium helveticum	82.3279	1042	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002102155.1	s__Mycobacterium europaeum	82.3038	1168	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001953985.1	s__Mycobacterium colombiense_B	82.2394	1229	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001053185.1	s__Mycobacterium bohemicum	82.221	1140	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_001667775.1	s__Mycobacterium sp001667775	81.9627	1047	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665875.1	s__Mycobacterium sp001665875	81.7433	1104	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247635.1	s__Mycobacterium sp019247635	81.6567	1030	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665395.1	s__Mycobacterium sp001665395	81.4478	1165	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705925.1	s__Mycobacterium ostraviense	80.9911	1055	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.9198	1152	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_002086275.1	s__Mycobacterium intermedium	80.3634	1078	2021	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:42,017] [INFO] GTDB search result was written to GCF_002102095.1_ASM210209v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:42,017] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:42,021] [INFO] DFAST_QC result json was written to GCF_002102095.1_ASM210209v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:42,021] [INFO] DFAST_QC completed!
[2024-01-25 18:53:42,021] [INFO] Total running time: 0h2m36s