[2024-01-24 11:05:25,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,440] [INFO] DQC Reference Directory: /var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference
[2024-01-24 11:05:26,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,881] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg325b1e91-04cc-49df-94c0-ebdc4bf2e1d8/GCF_003667315.2_ASM366731v2_genomic.fna.gz | prodigal -d GCF_003667315.2_ASM366731v2_genomic.fna/cds.fna -a GCF_003667315.2_ASM366731v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:42,748] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:42,749] [INFO] Task started: HMMsearch
[2024-01-24 11:05:42,749] [INFO] Running command: hmmsearch --tblout GCF_003667315.2_ASM366731v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference/reference_markers.hmm GCF_003667315.2_ASM366731v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:43,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:43,043] [INFO] Found 6/6 markers.
[2024-01-24 11:05:43,091] [INFO] Query marker FASTA was written to GCF_003667315.2_ASM366731v2_genomic.fna/markers.fasta
[2024-01-24 11:05:43,092] [INFO] Task started: Blastn
[2024-01-24 11:05:43,092] [INFO] Running command: blastn -query GCF_003667315.2_ASM366731v2_genomic.fna/markers.fasta -db /var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference/reference_markers.fasta -out GCF_003667315.2_ASM366731v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:44,082] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:44,086] [INFO] Selected 22 target genomes.
[2024-01-24 11:05:44,087] [INFO] Target genome list was writen to GCF_003667315.2_ASM366731v2_genomic.fna/target_genomes.txt
[2024-01-24 11:05:44,096] [INFO] Task started: fastANI
[2024-01-24 11:05:44,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg325b1e91-04cc-49df-94c0-ebdc4bf2e1d8/GCF_003667315.2_ASM366731v2_genomic.fna.gz --refList GCF_003667315.2_ASM366731v2_genomic.fna/target_genomes.txt --output GCF_003667315.2_ASM366731v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:03,974] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:03,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:03,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:03,994] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:03,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:03,995] [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
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	80.0256	881	1649	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	80.025	867	1649	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.8373	710	1649	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.8258	668	1649	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.7886	716	1649	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.7563	680	1649	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	79.6122	764	1649	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.342	565	1649	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.2679	704	1649	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.159	610	1649	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	79.0336	628	1649	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.807	527	1649	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	78.5223	540	1649	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.489	524	1649	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	78.3903	446	1649	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	78.3635	539	1649	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.353	444	1649	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3342	485	1649	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.3113	423	1649	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.3022	502	1649	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	78.1918	479	1649	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.0549	437	1649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:03,997] [INFO] DFAST Taxonomy check result was written to GCF_003667315.2_ASM366731v2_genomic.fna/tc_result.tsv
[2024-01-24 11:06:03,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:03,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:03,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference/checkm_data
[2024-01-24 11:06:03,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:04,047] [INFO] Task started: CheckM
[2024-01-24 11:06:04,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667315.2_ASM366731v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667315.2_ASM366731v2_genomic.fna/checkm_input GCF_003667315.2_ASM366731v2_genomic.fna/checkm_result
[2024-01-24 11:06:58,385] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:58,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:58,412] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:58,412] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:58,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667315.2_ASM366731v2_genomic.fna/markers.fasta)
[2024-01-24 11:06:58,413] [INFO] Task started: Blastn
[2024-01-24 11:06:58,414] [INFO] Running command: blastn -query GCF_003667315.2_ASM366731v2_genomic.fna/markers.fasta -db /var/lib/cwl/stged4345b2-d7f1-45dd-a564-7e3e93ab940b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667315.2_ASM366731v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:00,048] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:00,053] [INFO] Selected 15 target genomes.
[2024-01-24 11:07:00,053] [INFO] Target genome list was writen to GCF_003667315.2_ASM366731v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:00,066] [INFO] Task started: fastANI
[2024-01-24 11:07:00,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg325b1e91-04cc-49df-94c0-ebdc4bf2e1d8/GCF_003667315.2_ASM366731v2_genomic.fna.gz --refList GCF_003667315.2_ASM366731v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003667315.2_ASM366731v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:15,959] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:15,977] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:15,977] [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_003667315.2	s__Tropicibacter sp003667315	100.0	1646	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176475.1	s__Tropicibacter naphthalenivorans	81.8072	901	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016806125.1	s__AWRV01 sp000504185	80.7688	832	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_017255395.1	s__AWRV01 sp017255395	80.7261	844	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.6155	852	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	80.2818	858	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	80.0171	868	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_000153725.1	s__Salipiger bermudensis	79.8464	708	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_000169415.1	s__Sagittula stellata	79.7572	762	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188425.1	s__Antarctobacter heliothermus	79.4621	749	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	79.2352	691	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_017813235.1	s__Sagittula sp017813235	79.154	710	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	79.0367	627	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	78.4551	537	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	78.2097	499	1649	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:15,979] [INFO] GTDB search result was written to GCF_003667315.2_ASM366731v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:15,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:15,984] [INFO] DFAST_QC result json was written to GCF_003667315.2_ASM366731v2_genomic.fna/dqc_result.json
[2024-01-24 11:07:15,984] [INFO] DFAST_QC completed!
[2024-01-24 11:07:15,984] [INFO] Total running time: 0h1m51s