[2024-01-24 11:05:24,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,411] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,412] [INFO] DQC Reference Directory: /var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference
[2024-01-24 11:05:26,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,029] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b6eb7e-c57c-453f-90f0-b7ac1ff99612/GCF_002157835.1_ASM215783v1_genomic.fna.gz | prodigal -d GCF_002157835.1_ASM215783v1_genomic.fna/cds.fna -a GCF_002157835.1_ASM215783v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:52,500] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:52,500] [INFO] Task started: HMMsearch
[2024-01-24 11:05:52,501] [INFO] Running command: hmmsearch --tblout GCF_002157835.1_ASM215783v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference/reference_markers.hmm GCF_002157835.1_ASM215783v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:52,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:52,864] [INFO] Found 6/6 markers.
[2024-01-24 11:05:52,933] [INFO] Query marker FASTA was written to GCF_002157835.1_ASM215783v1_genomic.fna/markers.fasta
[2024-01-24 11:05:52,933] [INFO] Task started: Blastn
[2024-01-24 11:05:52,933] [INFO] Running command: blastn -query GCF_002157835.1_ASM215783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference/reference_markers.fasta -out GCF_002157835.1_ASM215783v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:54,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:54,119] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:54,120] [INFO] Target genome list was writen to GCF_002157835.1_ASM215783v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:54,127] [INFO] Task started: fastANI
[2024-01-24 11:05:54,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b6eb7e-c57c-453f-90f0-b7ac1ff99612/GCF_002157835.1_ASM215783v1_genomic.fna.gz --refList GCF_002157835.1_ASM215783v1_genomic.fna/target_genomes.txt --output GCF_002157835.1_ASM215783v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:25,562] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:25,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:25,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:25,583] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:25,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:25,584] [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 dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	100.0	2688	2690	95	conclusive
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	92.7222	2047	2690	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	82.8054	1607	2690	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	82.7179	1630	2690	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	82.1551	1339	2690	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	82.125	1279	2690	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	82.0867	1312	2690	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	82.0855	1347	2690	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	82.0006	1164	2690	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	81.8444	1226	2690	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	81.7408	1276	2690	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	81.7123	1271	2690	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	81.6763	1266	2690	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.3938	923	2690	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.1503	627	2690	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.6231	876	2690	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5889	890	2690	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5386	897	2690	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.2476	693	2690	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.1726	829	2690	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	79.046	708	2690	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	78.9856	704	2690	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	78.8407	726	2690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:25,585] [INFO] DFAST Taxonomy check result was written to GCF_002157835.1_ASM215783v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:25,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:25,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:25,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference/checkm_data
[2024-01-24 11:06:25,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:25,662] [INFO] Task started: CheckM
[2024-01-24 11:06:25,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002157835.1_ASM215783v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002157835.1_ASM215783v1_genomic.fna/checkm_input GCF_002157835.1_ASM215783v1_genomic.fna/checkm_result
[2024-01-24 11:08:18,706] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:18,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:18,732] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:18,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:18,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002157835.1_ASM215783v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:18,733] [INFO] Task started: Blastn
[2024-01-24 11:08:18,733] [INFO] Running command: blastn -query GCF_002157835.1_ASM215783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd62e7f99-2508-408d-ae71-e226ee1c3584/dqc_reference/reference_markers_gtdb.fasta -out GCF_002157835.1_ASM215783v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:20,482] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:20,487] [INFO] Selected 19 target genomes.
[2024-01-24 11:08:20,487] [INFO] Target genome list was writen to GCF_002157835.1_ASM215783v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:20,524] [INFO] Task started: fastANI
[2024-01-24 11:08:20,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b6eb7e-c57c-453f-90f0-b7ac1ff99612/GCF_002157835.1_ASM215783v1_genomic.fna.gz --refList GCF_002157835.1_ASM215783v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002157835.1_ASM215783v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:48,579] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:48,594] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:48,594] [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_002157835.1	s__Mycobacterium dioxanotrophicus	100.0	2688	2690	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_002086485.1	s__Mycobacterium aquaticum	92.7186	2048	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665685.1	s__Mycobacterium sp001665685	91.2931	1957	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570425.1	s__Mycobacterium brisbanense	91.0324	1942	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.59	97.59	0.86	0.86	2	-
GCF_000382405.1	s__Mycobacterium sp000382405	86.1964	1210	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373905.1	s__Mycobacterium sp000373905	86.1095	1196	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	82.7999	1609	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_017876775.1	s__Mycobacterium lutetiense	82.3272	1276	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	82.2107	1288	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_010731295.1	s__Mycobacterium boenickei	82.1453	1341	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001942045.1	s__Mycobacterium porcinum_A	82.0585	1292	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295855.1	s__Mycobacterium fortuitum	81.8238	1231	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_002723835.1	s__Mycobacterium sp002723835	80.1883	897	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	80.1477	1065	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_011694515.1	s__Mycobacterium sp011694515	79.6365	819	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328565.1	s__Mycobacterium sp000328565	79.5334	956	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	79.4873	920	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	79.2008	912	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCF_002591975.1	s__Mycobacterium neglectum	79.0043	869	2690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:48,596] [INFO] GTDB search result was written to GCF_002157835.1_ASM215783v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:48,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:48,601] [INFO] DFAST_QC result json was written to GCF_002157835.1_ASM215783v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:48,601] [INFO] DFAST_QC completed!
[2024-01-24 11:08:48,601] [INFO] Total running time: 0h3m24s