[2024-01-24 13:47:10,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference
[2024-01-24 13:47:11,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:11,714] [INFO] Task started: Prodigal
[2024-01-24 13:47:11,714] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c233630-45b7-4256-a640-caa3c11fc3bc/GCF_014656415.1_ASM1465641v1_genomic.fna.gz | prodigal -d GCF_014656415.1_ASM1465641v1_genomic.fna/cds.fna -a GCF_014656415.1_ASM1465641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:27,589] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:27,589] [INFO] Task started: HMMsearch
[2024-01-24 13:47:27,589] [INFO] Running command: hmmsearch --tblout GCF_014656415.1_ASM1465641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference/reference_markers.hmm GCF_014656415.1_ASM1465641v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:27,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:27,902] [INFO] Found 6/6 markers.
[2024-01-24 13:47:27,952] [INFO] Query marker FASTA was written to GCF_014656415.1_ASM1465641v1_genomic.fna/markers.fasta
[2024-01-24 13:47:27,952] [INFO] Task started: Blastn
[2024-01-24 13:47:27,952] [INFO] Running command: blastn -query GCF_014656415.1_ASM1465641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference/reference_markers.fasta -out GCF_014656415.1_ASM1465641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:28,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:28,848] [INFO] Selected 32 target genomes.
[2024-01-24 13:47:28,849] [INFO] Target genome list was writen to GCF_014656415.1_ASM1465641v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:28,871] [INFO] Task started: fastANI
[2024-01-24 13:47:28,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c233630-45b7-4256-a640-caa3c11fc3bc/GCF_014656415.1_ASM1465641v1_genomic.fna.gz --refList GCF_014656415.1_ASM1465641v1_genomic.fna/target_genomes.txt --output GCF_014656415.1_ASM1465641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:55,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:55,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:55,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:55,181] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:47:55,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:47:55,182] [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
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.1223	745	1802	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.9743	697	1802	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.9326	710	1802	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.6249	604	1802	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.5323	713	1802	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.5176	635	1802	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.4734	615	1802	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.1741	618	1802	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	79.133	636	1802	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	79.1103	653	1802	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.0754	633	1802	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	79.0406	659	1802	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.0289	630	1802	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.9752	537	1802	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.975	566	1802	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.9574	643	1802	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.9546	583	1802	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.84	593	1802	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	78.8285	537	1802	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.8229	543	1802	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.7897	545	1802	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.6948	579	1802	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.6235	546	1802	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5946	520	1802	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	78.4747	388	1802	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.1829	410	1802	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0701	422	1802	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	78.0185	437	1802	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	77.695	547	1802	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6365	394	1802	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.5061	354	1802	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.4429	322	1802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:55,184] [INFO] DFAST Taxonomy check result was written to GCF_014656415.1_ASM1465641v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:55,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:55,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:55,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference/checkm_data
[2024-01-24 13:47:55,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:55,235] [INFO] Task started: CheckM
[2024-01-24 13:47:55,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656415.1_ASM1465641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656415.1_ASM1465641v1_genomic.fna/checkm_input GCF_014656415.1_ASM1465641v1_genomic.fna/checkm_result
[2024-01-24 13:48:44,276] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:44,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:44,298] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:44,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:44,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656415.1_ASM1465641v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:44,300] [INFO] Task started: Blastn
[2024-01-24 13:48:44,300] [INFO] Running command: blastn -query GCF_014656415.1_ASM1465641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6785dc6e-d48e-40e3-aaaa-36fee7ae8789/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656415.1_ASM1465641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:45,808] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:45,813] [INFO] Selected 22 target genomes.
[2024-01-24 13:48:45,813] [INFO] Target genome list was writen to GCF_014656415.1_ASM1465641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:45,836] [INFO] Task started: fastANI
[2024-01-24 13:48:45,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c233630-45b7-4256-a640-caa3c11fc3bc/GCF_014656415.1_ASM1465641v1_genomic.fna.gz --refList GCF_014656415.1_ASM1465641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656415.1_ASM1465641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:07,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:07,506] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:07,507] [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_014656415.1	s__Seohaeicola zhoushanensis	100.0	1799	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003116585.1	s__Albibacillus kandeliae	80.7388	927	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.6139	726	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	80.0804	751	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.9518	708	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001507595.1	s__Ruegeria marisrubri	79.6762	621	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.5998	607	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.5697	705	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_001969385.1	s__Salipiger profundus	79.5252	634	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900129345.1	s__Ruegeria intermedia	79.4624	616	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.3522	673	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.2092	662	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	79.1404	636	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002814095.1	s__Sagittula sp002814095	79.0561	659	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	79.0442	630	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_017311415.1	s__Salipiger abyssi_A	79.0436	625	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765275.1	s__Chachezhania sp009765275	79.0403	659	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	78.9917	577	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.9748	566	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000521865.1	s__Roseivivax isoporae	78.813	598	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054175.1	s__Allosediminivita pacifica	78.7864	546	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000169415.1	s__Sagittula stellata	78.6727	558	1802	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:07,508] [INFO] GTDB search result was written to GCF_014656415.1_ASM1465641v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:07,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:07,514] [INFO] DFAST_QC result json was written to GCF_014656415.1_ASM1465641v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:07,515] [INFO] DFAST_QC completed!
[2024-01-24 13:49:07,515] [INFO] Total running time: 0h1m57s