[2024-01-25 18:11:50,351] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:50,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:50,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference
[2024-01-25 18:11:51,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:51,501] [INFO] Task started: Prodigal
[2024-01-25 18:11:51,501] [INFO] Running command: gunzip -c /var/lib/cwl/stgc081d6b9-6175-4345-98be-51ac954a68b4/GCF_000422945.1_ASM42294v1_genomic.fna.gz | prodigal -d GCF_000422945.1_ASM42294v1_genomic.fna/cds.fna -a GCF_000422945.1_ASM42294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:01,635] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:01,635] [INFO] Task started: HMMsearch
[2024-01-25 18:12:01,635] [INFO] Running command: hmmsearch --tblout GCF_000422945.1_ASM42294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference/reference_markers.hmm GCF_000422945.1_ASM42294v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:01,867] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:01,868] [INFO] Found 6/6 markers.
[2024-01-25 18:12:01,895] [INFO] Query marker FASTA was written to GCF_000422945.1_ASM42294v1_genomic.fna/markers.fasta
[2024-01-25 18:12:01,895] [INFO] Task started: Blastn
[2024-01-25 18:12:01,895] [INFO] Running command: blastn -query GCF_000422945.1_ASM42294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference/reference_markers.fasta -out GCF_000422945.1_ASM42294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:02,462] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:02,465] [INFO] Selected 23 target genomes.
[2024-01-25 18:12:02,465] [INFO] Target genome list was writen to GCF_000422945.1_ASM42294v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:02,478] [INFO] Task started: fastANI
[2024-01-25 18:12:02,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgc081d6b9-6175-4345-98be-51ac954a68b4/GCF_000422945.1_ASM42294v1_genomic.fna.gz --refList GCF_000422945.1_ASM42294v1_genomic.fna/target_genomes.txt --output GCF_000422945.1_ASM42294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:22,866] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:22,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:22,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:22,878] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:22,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:22,879] [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
Daejeonella oryzae	strain=DSM 19973	GCA_000422945.1	1122943	1122943	type	True	100.0	1141	1142	95	conclusive
Flavihumibacter soli	strain=R14	GCA_010692725.1	2705549	2705549	type	True	77.9301	163	1142	95	below_threshold
Daejeonella rubra	strain=DSM 24536	GCA_900103545.1	990371	990371	type	True	77.4727	168	1142	95	below_threshold
Daejeonella lutea	strain=DSM 22385	GCA_900168015.1	572036	572036	type	True	77.2758	119	1142	95	below_threshold
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	76.904	60	1142	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	76.8436	87	1142	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_003313385.1	2233776	2233776	type	True	76.8408	52	1142	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	76.8408	52	1142	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	76.8249	89	1142	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	76.779	69	1142	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	76.7518	75	1142	95	below_threshold
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	76.7409	85	1142	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	76.7265	68	1142	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	76.6709	82	1142	95	below_threshold
Pedobacter rhizosphaerae	strain=DSM 18610	GCA_900111155.1	390241	390241	type	True	76.6588	75	1142	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	76.6576	81	1142	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	76.6425	67	1142	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	76.4871	70	1142	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	76.3598	65	1142	95	below_threshold
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	76.1099	91	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:22,880] [INFO] DFAST Taxonomy check result was written to GCF_000422945.1_ASM42294v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:22,881] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:22,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:22,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference/checkm_data
[2024-01-25 18:12:22,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:22,918] [INFO] Task started: CheckM
[2024-01-25 18:12:22,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422945.1_ASM42294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422945.1_ASM42294v1_genomic.fna/checkm_input GCF_000422945.1_ASM42294v1_genomic.fna/checkm_result
[2024-01-25 18:12:55,382] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:55,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:55,401] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:55,401] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:55,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422945.1_ASM42294v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:55,401] [INFO] Task started: Blastn
[2024-01-25 18:12:55,401] [INFO] Running command: blastn -query GCF_000422945.1_ASM42294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c715d29-132e-4ef3-9bd4-55e20f51d1a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422945.1_ASM42294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:56,269] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:56,274] [INFO] Selected 24 target genomes.
[2024-01-25 18:12:56,274] [INFO] Target genome list was writen to GCF_000422945.1_ASM42294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:56,295] [INFO] Task started: fastANI
[2024-01-25 18:12:56,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgc081d6b9-6175-4345-98be-51ac954a68b4/GCF_000422945.1_ASM42294v1_genomic.fna.gz --refList GCF_000422945.1_ASM42294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422945.1_ASM42294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:14,046] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:14,060] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:14,060] [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_000422945.1	s__Daejeonella oryzae	100.0	1141	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010692725.1	s__Daejeonella soli	77.9301	163	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017495225.1	s__Daejeonella sp017495225	77.7613	109	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103545.1	s__Daejeonella rubra	77.4727	168	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257025.1	s__Daejeonella sp002257025	77.446	129	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009834875.1	s__HMF7647 sp009834875	77.3136	88	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168015.1	s__Daejeonella lutea	77.2758	119	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635725.1	s__Pedobacter mendelii	77.1162	71	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421515.1	s__Pedobacter sp001421515	77.0574	79	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378705.1	s__Daejeonella sp014378705	77.0367	160	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274585.1	s__BS3 sp008274585	77.0336	66	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__BS3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636695.1	s__Pedobacter panaciterrae_A	76.9167	92	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221995.1	s__Mucilaginibacter boryungensis	76.904	60	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708265.2	s__Pedobacter sp000708265	76.8296	78	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342125.1	s__Pedobacter sp004342125	76.7971	84	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_003259615.1	s__Pedobacter cryoconitis	76.7265	68	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111155.1	s__Pedobacter rhizosphaerae	76.6566	74	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	76.6275	92	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	76.5718	63	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868395.1	s__Daejeonella sp016868395	76.4146	99	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821625.1	s__Daejeonella sp903821625	76.3358	92	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754915.1	s__Mucilaginibacter_A arboris	76.2242	75	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927645.1	s__Mucilaginibacter sp903927645	75.8433	64	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.68	99.68	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:14,061] [INFO] GTDB search result was written to GCF_000422945.1_ASM42294v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:14,062] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:14,066] [INFO] DFAST_QC result json was written to GCF_000422945.1_ASM42294v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:14,066] [INFO] DFAST_QC completed!
[2024-01-25 18:13:14,067] [INFO] Total running time: 0h1m24s