[2024-01-24 13:58:25,518] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference
[2024-01-24 13:58:26,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,965] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e7e015d-5432-4669-a28d-3a83a31729c6/GCF_020529025.1_ASM2052902v1_genomic.fna.gz | prodigal -d GCF_020529025.1_ASM2052902v1_genomic.fna/cds.fna -a GCF_020529025.1_ASM2052902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:42,220] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:42,221] [INFO] Task started: HMMsearch
[2024-01-24 13:58:42,221] [INFO] Running command: hmmsearch --tblout GCF_020529025.1_ASM2052902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference/reference_markers.hmm GCF_020529025.1_ASM2052902v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:42,507] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:42,508] [INFO] Found 6/6 markers.
[2024-01-24 13:58:42,555] [INFO] Query marker FASTA was written to GCF_020529025.1_ASM2052902v1_genomic.fna/markers.fasta
[2024-01-24 13:58:42,556] [INFO] Task started: Blastn
[2024-01-24 13:58:42,556] [INFO] Running command: blastn -query GCF_020529025.1_ASM2052902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference/reference_markers.fasta -out GCF_020529025.1_ASM2052902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,482] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,486] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:43,486] [INFO] Target genome list was writen to GCF_020529025.1_ASM2052902v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:43,503] [INFO] Task started: fastANI
[2024-01-24 13:58:43,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7e015d-5432-4669-a28d-3a83a31729c6/GCF_020529025.1_ASM2052902v1_genomic.fna.gz --refList GCF_020529025.1_ASM2052902v1_genomic.fna/target_genomes.txt --output GCF_020529025.1_ASM2052902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:01,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:01,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:01,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:01,420] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:01,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:01,421] [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
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	100.0	1508	1512	95	conclusive
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	78.9004	525	1512	95	below_threshold
Oceaniglobus ichthyenteri	strain=YLY08	GCA_003057885.1	2136177	2136177	type	True	78.7872	552	1512	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.7828	368	1512	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	78.7753	533	1512	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.5592	432	1512	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.46	415	1512	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.4115	425	1512	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.3795	435	1512	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.3079	427	1512	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	78.2804	426	1512	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2765	430	1512	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2426	436	1512	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.2161	421	1512	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1889	461	1512	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.177	439	1512	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.0513	411	1512	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.9999	379	1512	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.9471	383	1512	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.7283	386	1512	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	77.6888	390	1512	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.6869	359	1512	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.5242	365	1512	95	below_threshold
Rhodovulum imhoffii	strain=DSM 18064	GCA_016653305.1	365340	365340	type	True	77.2692	223	1512	95	below_threshold
Rhodovulum imhoffii	strain=DSM 18064	GCA_003046545.1	365340	365340	type	True	77.168	220	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:01,422] [INFO] DFAST Taxonomy check result was written to GCF_020529025.1_ASM2052902v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:01,423] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:01,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:01,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference/checkm_data
[2024-01-24 13:59:01,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:01,469] [INFO] Task started: CheckM
[2024-01-24 13:59:01,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020529025.1_ASM2052902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020529025.1_ASM2052902v1_genomic.fna/checkm_input GCF_020529025.1_ASM2052902v1_genomic.fna/checkm_result
[2024-01-24 13:59:53,488] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:53,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:53,508] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:53,508] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:53,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020529025.1_ASM2052902v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:53,509] [INFO] Task started: Blastn
[2024-01-24 13:59:53,509] [INFO] Running command: blastn -query GCF_020529025.1_ASM2052902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7b3134-3119-4011-bbc7-36d5edfddbfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_020529025.1_ASM2052902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:55,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:55,028] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:55,028] [INFO] Target genome list was writen to GCF_020529025.1_ASM2052902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:55,058] [INFO] Task started: fastANI
[2024-01-24 13:59:55,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7e015d-5432-4669-a28d-3a83a31729c6/GCF_020529025.1_ASM2052902v1_genomic.fna.gz --refList GCF_020529025.1_ASM2052902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020529025.1_ASM2052902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:06,955] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:06,968] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:00:06,969] [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
GCA_009992615.1	s__Oceaniglobus sp009992615	80.3864	423	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002751875.1	s__Oceaniglobus indicus	80.2273	664	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	79.8273	724	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008085915.1	s__Oceaniglobus sp008085915	79.2438	660	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.9699	514	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	78.861	502	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057885.1	s__Oceaniglobus ichthyenteri	78.7874	552	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.5488	433	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCA_003511785.1	s__UBA7951 sp003511785	78.4298	340	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086115.1	s__Muriiphilus fusiformis	78.3176	465	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	98.34	98.34	0.92	0.92	2	-
GCF_001482405.1	s__Ponticoccus marisrubri	78.2943	565	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	78.1671	503	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	78.1535	312	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	77.7453	384	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003575965.1	s__Pseudooceanicola sediminis	77.7178	386	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCF_013868135.1	s__Paracoccus sp013868135	77.5672	303	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:06,970] [INFO] GTDB search result was written to GCF_020529025.1_ASM2052902v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:06,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:06,976] [INFO] DFAST_QC result json was written to GCF_020529025.1_ASM2052902v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:06,976] [INFO] DFAST_QC completed!
[2024-01-24 14:00:06,976] [INFO] Total running time: 0h1m41s