[2023-06-27 13:03:58,248] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:03:58,250] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:03:58,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference
[2023-06-27 13:03:59,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:03:59,427] [INFO] Task started: Prodigal
[2023-06-27 13:03:59,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ad29888-2d20-4c1f-9527-b2cbe5d06214/GCA_026224835.1_ASM2622483v1_genomic.fna.gz | prodigal -d GCA_026224835.1_ASM2622483v1_genomic.fna/cds.fna -a GCA_026224835.1_ASM2622483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:04:23,899] [INFO] Task succeeded: Prodigal
[2023-06-27 13:04:23,900] [INFO] Task started: HMMsearch
[2023-06-27 13:04:23,900] [INFO] Running command: hmmsearch --tblout GCA_026224835.1_ASM2622483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference/reference_markers.hmm GCA_026224835.1_ASM2622483v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:04:24,154] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:04:24,155] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ad29888-2d20-4c1f-9527-b2cbe5d06214/GCA_026224835.1_ASM2622483v1_genomic.fna.gz]
[2023-06-27 13:04:24,201] [INFO] Query marker FASTA was written to GCA_026224835.1_ASM2622483v1_genomic.fna/markers.fasta
[2023-06-27 13:04:24,202] [INFO] Task started: Blastn
[2023-06-27 13:04:24,202] [INFO] Running command: blastn -query GCA_026224835.1_ASM2622483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference/reference_markers.fasta -out GCA_026224835.1_ASM2622483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:04:24,771] [INFO] Task succeeded: Blastn
[2023-06-27 13:04:24,775] [INFO] Selected 24 target genomes.
[2023-06-27 13:04:24,776] [INFO] Target genome list was writen to GCA_026224835.1_ASM2622483v1_genomic.fna/target_genomes.txt
[2023-06-27 13:04:24,782] [INFO] Task started: fastANI
[2023-06-27 13:04:24,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad29888-2d20-4c1f-9527-b2cbe5d06214/GCA_026224835.1_ASM2622483v1_genomic.fna.gz --refList GCA_026224835.1_ASM2622483v1_genomic.fna/target_genomes.txt --output GCA_026224835.1_ASM2622483v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:04:43,559] [INFO] Task succeeded: fastANI
[2023-06-27 13:04:43,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:04:43,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:04:43,575] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 13:04:43,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 13:04:43,575] [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
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	91.8212	1523	2069	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	78.111	415	2069	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.3559	393	2069	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.3299	356	2069	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.3066	357	2069	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	77.3043	369	2069	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.1967	282	2069	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.0678	334	2069	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	76.9949	290	2069	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.9519	293	2069	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	76.8969	306	2069	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	76.8939	205	2069	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	76.8466	308	2069	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.8312	255	2069	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	76.6655	236	2069	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	76.6546	212	2069	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	76.6492	217	2069	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.6042	189	2069	95	below_threshold
Mucilaginibacter ginsenosidivorans	strain=Gsoil 3017	GCA_007971025.1	398053	398053	type	True	76.2559	206	2069	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 13:04:43,577] [INFO] DFAST Taxonomy check result was written to GCA_026224835.1_ASM2622483v1_genomic.fna/tc_result.tsv
[2023-06-27 13:04:43,578] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:04:43,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:04:43,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference/checkm_data
[2023-06-27 13:04:43,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:04:43,637] [INFO] Task started: CheckM
[2023-06-27 13:04:43,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026224835.1_ASM2622483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026224835.1_ASM2622483v1_genomic.fna/checkm_input GCA_026224835.1_ASM2622483v1_genomic.fna/checkm_result
[2023-06-27 13:05:51,026] [INFO] Task succeeded: CheckM
[2023-06-27 13:05:51,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 13:05:51,047] [INFO] ===== Completeness check finished =====
[2023-06-27 13:05:51,047] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:05:51,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026224835.1_ASM2622483v1_genomic.fna/markers.fasta)
[2023-06-27 13:05:51,048] [INFO] Task started: Blastn
[2023-06-27 13:05:51,048] [INFO] Running command: blastn -query GCA_026224835.1_ASM2622483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad718cc-7385-4313-9c0b-d4b0e492cd08/dqc_reference/reference_markers_gtdb.fasta -out GCA_026224835.1_ASM2622483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:05:51,826] [INFO] Task succeeded: Blastn
[2023-06-27 13:05:51,881] [INFO] Selected 17 target genomes.
[2023-06-27 13:05:51,882] [INFO] Target genome list was writen to GCA_026224835.1_ASM2622483v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:05:51,893] [INFO] Task started: fastANI
[2023-06-27 13:05:51,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad29888-2d20-4c1f-9527-b2cbe5d06214/GCA_026224835.1_ASM2622483v1_genomic.fna.gz --refList GCA_026224835.1_ASM2622483v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026224835.1_ASM2622483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:06:05,826] [INFO] Task succeeded: fastANI
[2023-06-27 13:06:05,837] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 13:06:05,837] [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_014200495.1	s__Mucilaginibacter sp014200495	97.9801	1710	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900105165.1	s__Mucilaginibacter mallensis	91.8099	1524	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	79.68	707	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013287375.1	s__Mucilaginibacter sp013287375	79.1852	380	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.48	99.44	0.60	0.60	3	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	78.7258	492	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	78.5252	465	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	77.2214	420	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	77.1955	282	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885865.1	s__Mucilaginibacter sp903885865	77.173	179	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.00	99.00	0.77	0.77	2	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	76.9816	279	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	76.8477	291	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971025.1	s__Mucilaginibacter ginsenosidivorans	76.2407	209	2069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:06:05,839] [INFO] GTDB search result was written to GCA_026224835.1_ASM2622483v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:06:05,839] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:06:05,843] [INFO] DFAST_QC result json was written to GCA_026224835.1_ASM2622483v1_genomic.fna/dqc_result.json
[2023-06-27 13:06:05,843] [INFO] DFAST_QC completed!
[2023-06-27 13:06:05,844] [INFO] Total running time: 0h2m8s