[2024-01-24 13:17:41,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:41,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:41,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference
[2024-01-24 13:17:42,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:42,888] [INFO] Task started: Prodigal
[2024-01-24 13:17:42,888] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe33dacc-e9ba-4f18-813d-67898be006ac/GCF_003054175.1_ASM305417v1_genomic.fna.gz | prodigal -d GCF_003054175.1_ASM305417v1_genomic.fna/cds.fna -a GCF_003054175.1_ASM305417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:56,683] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:56,684] [INFO] Task started: HMMsearch
[2024-01-24 13:17:56,684] [INFO] Running command: hmmsearch --tblout GCF_003054175.1_ASM305417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference/reference_markers.hmm GCF_003054175.1_ASM305417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:56,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:56,964] [INFO] Found 6/6 markers.
[2024-01-24 13:17:57,008] [INFO] Query marker FASTA was written to GCF_003054175.1_ASM305417v1_genomic.fna/markers.fasta
[2024-01-24 13:17:57,008] [INFO] Task started: Blastn
[2024-01-24 13:17:57,008] [INFO] Running command: blastn -query GCF_003054175.1_ASM305417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference/reference_markers.fasta -out GCF_003054175.1_ASM305417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:57,866] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:57,869] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:57,870] [INFO] Target genome list was writen to GCF_003054175.1_ASM305417v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:57,915] [INFO] Task started: fastANI
[2024-01-24 13:17:57,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe33dacc-e9ba-4f18-813d-67898be006ac/GCF_003054175.1_ASM305417v1_genomic.fna.gz --refList GCF_003054175.1_ASM305417v1_genomic.fna/target_genomes.txt --output GCF_003054175.1_ASM305417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:15,830] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:15,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:15,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:15,846] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:15,846] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:15,847] [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
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	100.0	1561	1565	95	conclusive
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	99.9951	1546	1565	95	conclusive
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.9112	714	1565	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	80.1673	729	1565	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	80.0562	705	1565	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.9335	688	1565	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.7727	646	1565	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.2341	538	1565	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.1998	625	1565	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.1389	545	1565	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.1274	559	1565	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.623	499	1565	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.6104	497	1565	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.599	491	1565	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.4403	477	1565	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.3571	372	1565	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2704	373	1565	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.2124	439	1565	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.0546	449	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,848] [INFO] DFAST Taxonomy check result was written to GCF_003054175.1_ASM305417v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:15,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:15,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:15,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference/checkm_data
[2024-01-24 13:18:15,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:15,899] [INFO] Task started: CheckM
[2024-01-24 13:18:15,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003054175.1_ASM305417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003054175.1_ASM305417v1_genomic.fna/checkm_input GCF_003054175.1_ASM305417v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,073] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,096] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003054175.1_ASM305417v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,098] [INFO] Task started: Blastn
[2024-01-24 13:19:00,098] [INFO] Running command: blastn -query GCF_003054175.1_ASM305417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b395a6d-81c1-4d5a-9a45-f18fad8d38c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003054175.1_ASM305417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,590] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:01,590] [INFO] Target genome list was writen to GCF_003054175.1_ASM305417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,615] [INFO] Task started: fastANI
[2024-01-24 13:19:01,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe33dacc-e9ba-4f18-813d-67898be006ac/GCF_003054175.1_ASM305417v1_genomic.fna.gz --refList GCF_003054175.1_ASM305417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003054175.1_ASM305417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:22,757] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:22,782] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:22,782] [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_003054175.1	s__Allosediminivita pacifica	100.0	1561	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000442255.1	s__Salipiger mucosus	81.3043	727	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	80.9015	746	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900102075.1	s__Salipiger thiooxidans	80.1864	726	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_900107235.1	s__Citreimonas salinaria	80.1622	630	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	80.0799	702	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.0572	700	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	80.0163	520	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	79.9257	689	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_015223355.1	s__Salipiger pacificus_B	79.8973	690	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	79.8423	681	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.7664	646	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	79.7152	675	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	79.6822	650	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_003344785.1	s__Puniceibacterium profundi	79.6731	626	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111315.1	s__Tranquillimonas rosea	79.4588	535	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	79.3511	666	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.3493	529	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	79.2213	540	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000169415.1	s__Sagittula stellata	79.1642	569	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	79.0328	440	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.6099	497	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:22,784] [INFO] GTDB search result was written to GCF_003054175.1_ASM305417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:22,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:22,791] [INFO] DFAST_QC result json was written to GCF_003054175.1_ASM305417v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:22,792] [INFO] DFAST_QC completed!
[2024-01-24 13:19:22,792] [INFO] Total running time: 0h1m41s