[2024-01-24 13:12:39,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:39,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:39,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference
[2024-01-24 13:12:40,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,531] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e56274-29ae-473e-8599-8a656dfea8f9/GCF_017152025.1_ASM1715202v1_genomic.fna.gz | prodigal -d GCF_017152025.1_ASM1715202v1_genomic.fna/cds.fna -a GCF_017152025.1_ASM1715202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:55,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:55,269] [INFO] Task started: HMMsearch
[2024-01-24 13:12:55,270] [INFO] Running command: hmmsearch --tblout GCF_017152025.1_ASM1715202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference/reference_markers.hmm GCF_017152025.1_ASM1715202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:55,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:55,587] [INFO] Found 6/6 markers.
[2024-01-24 13:12:55,627] [INFO] Query marker FASTA was written to GCF_017152025.1_ASM1715202v1_genomic.fna/markers.fasta
[2024-01-24 13:12:55,628] [INFO] Task started: Blastn
[2024-01-24 13:12:55,628] [INFO] Running command: blastn -query GCF_017152025.1_ASM1715202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference/reference_markers.fasta -out GCF_017152025.1_ASM1715202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:56,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:56,420] [INFO] Selected 19 target genomes.
[2024-01-24 13:12:56,420] [INFO] Target genome list was writen to GCF_017152025.1_ASM1715202v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:56,428] [INFO] Task started: fastANI
[2024-01-24 13:12:56,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e56274-29ae-473e-8599-8a656dfea8f9/GCF_017152025.1_ASM1715202v1_genomic.fna.gz --refList GCF_017152025.1_ASM1715202v1_genomic.fna/target_genomes.txt --output GCF_017152025.1_ASM1715202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:13,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:13,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:13,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:13,635] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:13,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:13,635] [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
Hoyosella rhizosphaerae	strain=J12GA03	GCA_017152025.1	1755582	1755582	type	True	100.0	1170	1173	95	conclusive
Hoyosella rhizosphaerae	strain=CGMCC 1.15478	GCA_014643175.1	1755582	1755582	type	True	99.9987	1172	1173	95	conclusive
Hoyosella suaedae	strain=LNNU 331112	GCA_008312885.1	2605429	2605429	type	True	78.027	268	1173	95	below_threshold
Hoyosella subflava	strain=DQS3-9A1	GCA_000214175.1	639313	639313	type	True	77.7655	170	1173	95	below_threshold
Hoyosella altamirensis	strain=DSM 45258	GCA_014191505.1	616997	616997	type	True	77.7468	164	1173	95	below_threshold
Millisia brevis	strain=NBRC 105863	GCA_001552615.1	264148	264148	type	True	76.779	69	1173	95	below_threshold
Rhodococcus spongiicola	strain=LHW50502	GCA_004011835.1	2487352	2487352	type	True	76.7507	74	1173	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	76.5853	100	1173	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	76.5706	94	1173	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	76.5703	93	1173	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	76.5633	101	1173	95	below_threshold
Rhodococcus oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	76.4688	95	1173	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	76.4249	95	1173	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	76.3773	66	1173	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	76.3725	54	1173	95	below_threshold
Mycolicibacterium tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	76.1033	61	1173	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	75.9954	57	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:13,638] [INFO] DFAST Taxonomy check result was written to GCF_017152025.1_ASM1715202v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:13,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:13,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:13,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference/checkm_data
[2024-01-24 13:13:13,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:13,677] [INFO] Task started: CheckM
[2024-01-24 13:13:13,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017152025.1_ASM1715202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017152025.1_ASM1715202v1_genomic.fna/checkm_input GCF_017152025.1_ASM1715202v1_genomic.fna/checkm_result
[2024-01-24 13:13:59,301] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:59,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:59,323] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:59,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:59,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017152025.1_ASM1715202v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:59,324] [INFO] Task started: Blastn
[2024-01-24 13:13:59,324] [INFO] Running command: blastn -query GCF_017152025.1_ASM1715202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d6b8c93-8015-47e5-8356-f6e17233708f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017152025.1_ASM1715202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,375] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,380] [INFO] Selected 24 target genomes.
[2024-01-24 13:14:00,380] [INFO] Target genome list was writen to GCF_017152025.1_ASM1715202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:00,408] [INFO] Task started: fastANI
[2024-01-24 13:14:00,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e56274-29ae-473e-8599-8a656dfea8f9/GCF_017152025.1_ASM1715202v1_genomic.fna.gz --refList GCF_017152025.1_ASM1715202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017152025.1_ASM1715202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:20,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:20,810] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:20,811] [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_014643175.1	s__Hoyosella rhizosphaerae	99.9987	1172	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008312885.1	s__Hoyosella sp008312885	78.027	268	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841105.1	s__Hoyosella sp014841105	77.8403	261	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214175.1	s__Hoyosella subflava	77.7655	170	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191505.1	s__Hoyosella altamirensis	77.7468	164	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	99.98	99.98	0.97	0.97	2	-
GCF_002245895.1	s__Rhodococcus sp002245895	76.9236	91	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	76.779	69	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011835.1	s__Rhodococcus sp004011835	76.7507	74	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	76.5851	100	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_000010805.1	s__Rhodococcus opacus_C	76.4562	107	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004328705.1	s__Rhodococcus sp004328705	76.4339	91	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	76.4249	95	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612615.1	s__Nocardia amikacinitolerans	76.4117	96	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_000455125.1	s__Mycobacterium sp000455125	76.4029	55	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_001954135.1	s__Mycobacterium sp001954135	76.3982	60	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758805.1	s__Mycobacterium fluoranthenivorans	76.3773	66	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	-
GCF_001665875.1	s__Mycobacterium sp001665875	76.3752	50	1173	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	76.3669	60	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_900105905.1	s__Rhodococcus koreensis	76.2573	115	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.00	98.46	0.87	0.80	4	-
GCF_008329645.1	s__Mycobacterium grossiae	76.159	71	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	-
GCF_001373395.1	s__Mycobacterium lentiflavum	76.0561	59	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726205.1	s__Rhodococcus sp012726205	76.0557	81	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477355.1	s__Nocardia blacklockiae	76.0447	82	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:20,812] [INFO] GTDB search result was written to GCF_017152025.1_ASM1715202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:20,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:20,817] [INFO] DFAST_QC result json was written to GCF_017152025.1_ASM1715202v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:20,818] [INFO] DFAST_QC completed!
[2024-01-24 13:14:20,818] [INFO] Total running time: 0h1m42s