[2024-01-24 13:21:55,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:55,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:55,134] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference
[2024-01-24 13:21:56,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:56,395] [INFO] Task started: Prodigal
[2024-01-24 13:21:56,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg63b30c6c-91a6-4ee5-b333-ba872f503a27/GCF_010727475.1_ASM1072747v1_genomic.fna.gz | prodigal -d GCF_010727475.1_ASM1072747v1_genomic.fna/cds.fna -a GCF_010727475.1_ASM1072747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:23,273] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:23,274] [INFO] Task started: HMMsearch
[2024-01-24 13:22:23,274] [INFO] Running command: hmmsearch --tblout GCF_010727475.1_ASM1072747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference/reference_markers.hmm GCF_010727475.1_ASM1072747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:23,659] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:23,660] [INFO] Found 6/6 markers.
[2024-01-24 13:22:23,725] [INFO] Query marker FASTA was written to GCF_010727475.1_ASM1072747v1_genomic.fna/markers.fasta
[2024-01-24 13:22:23,725] [INFO] Task started: Blastn
[2024-01-24 13:22:23,725] [INFO] Running command: blastn -query GCF_010727475.1_ASM1072747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference/reference_markers.fasta -out GCF_010727475.1_ASM1072747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:24,976] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:24,981] [INFO] Selected 21 target genomes.
[2024-01-24 13:22:24,981] [INFO] Target genome list was writen to GCF_010727475.1_ASM1072747v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:25,078] [INFO] Task started: fastANI
[2024-01-24 13:22:25,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b30c6c-91a6-4ee5-b333-ba872f503a27/GCF_010727475.1_ASM1072747v1_genomic.fna.gz --refList GCF_010727475.1_ASM1072747v1_genomic.fna/target_genomes.txt --output GCF_010727475.1_ASM1072747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:56,773] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:56,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:56,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:56,796] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:56,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:56,797] [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
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	100.0	2668	2668	95	conclusive
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	99.9851	2647	2668	95	conclusive
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	82.8373	1585	2668	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	82.7384	1607	2668	95	below_threshold
Mycolicibacterium wolinskyi	strain=ATCC 700010	GCA_002101965.1	59750	59750	type	True	82.7328	1572	2668	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	82.6104	1386	2668	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	82.5875	1441	2668	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	82.4552	1412	2668	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	82.4477	1413	2668	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	82.1548	1233	2668	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	82.1526	1313	2668	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	82.061	1326	2668	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	82.0153	1337	2668	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	81.8699	1193	2668	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.4451	1087	2668	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.4449	1101	2668	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.0649	947	2668	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	79.9586	927	2668	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5304	893	2668	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.5061	851	2668	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3103	893	2668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:56,798] [INFO] DFAST Taxonomy check result was written to GCF_010727475.1_ASM1072747v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:56,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:56,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:56,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference/checkm_data
[2024-01-24 13:22:56,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:56,871] [INFO] Task started: CheckM
[2024-01-24 13:22:56,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010727475.1_ASM1072747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010727475.1_ASM1072747v1_genomic.fna/checkm_input GCF_010727475.1_ASM1072747v1_genomic.fna/checkm_result
[2024-01-24 13:24:45,431] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:45,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:45,456] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:45,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:45,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010727475.1_ASM1072747v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:45,457] [INFO] Task started: Blastn
[2024-01-24 13:24:45,458] [INFO] Running command: blastn -query GCF_010727475.1_ASM1072747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6be31a5-a0d2-4974-8e9c-a47ed4ef5b4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_010727475.1_ASM1072747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:47,448] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:47,453] [INFO] Selected 22 target genomes.
[2024-01-24 13:24:47,453] [INFO] Target genome list was writen to GCF_010727475.1_ASM1072747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:48,040] [INFO] Task started: fastANI
[2024-01-24 13:24:48,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b30c6c-91a6-4ee5-b333-ba872f503a27/GCF_010727475.1_ASM1072747v1_genomic.fna.gz --refList GCF_010727475.1_ASM1072747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010727475.1_ASM1072747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:19,603] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:19,622] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:19,623] [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_010727475.1	s__Mycobacterium mageritense	100.0	2668	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	conclusive
GCF_002086485.1	s__Mycobacterium aquaticum	82.8203	1588	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101965.1	s__Mycobacterium wolinskyi	82.692	1581	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.70	97.70	0.86	0.86	2	-
GCF_001570425.1	s__Mycobacterium brisbanense	82.6694	1589	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.59	97.59	0.86	0.86	2	-
GCF_900078665.2	s__Mycobacterium houstonense	82.6395	1381	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942045.1	s__Mycobacterium porcinum_A	82.5964	1366	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	82.5846	1444	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001665685.1	s__Mycobacterium sp001665685	82.5592	1564	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001245615.1	s__Mycobacterium neworleansense	82.4867	1393	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	82.4473	1414	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_002086835.1	s__Mycobacterium porcinum	82.3848	1456	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	82.1711	1230	2668	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	82.0602	986	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665785.1	s__Mycobacterium peregrinum_A	82.0501	1389	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727325.1	s__Mycobacterium alvei	81.8778	1189	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876775.1	s__Mycobacterium lutetiense	81.8709	1229	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	81.6344	1361	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_001499965.1	s__Mycobacterium sp001499965	80.5906	1063	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	80.4709	1060	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	80.4539	1098	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002838065.1	s__Mycobacterium sp002838065	80.3684	1015	2668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218295.1	s__Mycobacterium litorale_B	80.3516	1074	2668	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 13:25:19,624] [INFO] GTDB search result was written to GCF_010727475.1_ASM1072747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:19,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:19,629] [INFO] DFAST_QC result json was written to GCF_010727475.1_ASM1072747v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:19,630] [INFO] DFAST_QC completed!
[2024-01-24 13:25:19,630] [INFO] Total running time: 0h3m24s