[2023-03-18 23:44:06,291] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference
[2023-03-18 23:44:07,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,523] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,523] [INFO] Running command: cat /var/lib/cwl/stg5d5c1d5e-91a4-4323-8527-32d571315c02/OceanDNA-b29554.fa | prodigal -d OceanDNA-b29554/cds.fna -a OceanDNA-b29554/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:23,509] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:23,509] [INFO] Task started: HMMsearch
[2023-03-18 23:44:23,509] [INFO] Running command: hmmsearch --tblout OceanDNA-b29554/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference/reference_markers.hmm OceanDNA-b29554/protein.faa > /dev/null
[2023-03-18 23:44:23,707] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:23,707] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5d5c1d5e-91a4-4323-8527-32d571315c02/OceanDNA-b29554.fa]
[2023-03-18 23:44:23,727] [INFO] Query marker FASTA was written to OceanDNA-b29554/markers.fasta
[2023-03-18 23:44:23,727] [INFO] Task started: Blastn
[2023-03-18 23:44:23,727] [INFO] Running command: blastn -query OceanDNA-b29554/markers.fasta -db /var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference/reference_markers.fasta -out OceanDNA-b29554/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:24,439] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:24,439] [INFO] Selected 14 target genomes.
[2023-03-18 23:44:24,440] [INFO] Target genome list was writen to OceanDNA-b29554/target_genomes.txt
[2023-03-18 23:44:24,456] [INFO] Task started: fastANI
[2023-03-18 23:44:24,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d5c1d5e-91a4-4323-8527-32d571315c02/OceanDNA-b29554.fa --refList OceanDNA-b29554/target_genomes.txt --output OceanDNA-b29554/fastani_result.tsv --threads 1
[2023-03-18 23:44:33,810] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:33,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:33,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:33,819] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:33,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:33,820] [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
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	79.3703	529	836	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	79.2009	517	836	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	78.7659	457	836	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0074	335	836	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.8512	337	836	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6425	244	836	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	77.5934	271	836	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.5275	322	836	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.4926	326	836	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.4072	282	836	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.3339	232	836	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.2367	258	836	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.1495	270	836	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1079	219	836	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:33,820] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29554/tc_result.tsv
[2023-03-18 23:44:33,820] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:33,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:33,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference/checkm_data
[2023-03-18 23:44:33,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:33,854] [INFO] Task started: CheckM
[2023-03-18 23:44:33,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29554/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29554/checkm_input OceanDNA-b29554/checkm_result
[2023-03-18 23:45:16,621] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:16,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:16,631] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:16,631] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:16,631] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29554/markers.fasta)
[2023-03-18 23:45:16,632] [INFO] Task started: Blastn
[2023-03-18 23:45:16,632] [INFO] Running command: blastn -query OceanDNA-b29554/markers.fasta -db /var/lib/cwl/stgfaa5cdc4-c4ee-4733-b0b7-38c3ee726171/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29554/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:17,908] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:17,913] [INFO] Selected 11 target genomes.
[2023-03-18 23:45:17,913] [INFO] Target genome list was writen to OceanDNA-b29554/target_genomes_gtdb.txt
[2023-03-18 23:45:17,921] [INFO] Task started: fastANI
[2023-03-18 23:45:17,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d5c1d5e-91a4-4323-8527-32d571315c02/OceanDNA-b29554.fa --refList OceanDNA-b29554/target_genomes_gtdb.txt --output OceanDNA-b29554/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:26,408] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:26,415] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:45:26,415] [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_013155465.1	s__Alterinioella nitratireducens	82.1253	643	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_004000255.1	s__Nioella ostreopsis	79.3801	528	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	79.1966	517	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001879715.1	s__Nioella nitratireducens	78.7662	457	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	78.6978	364	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	78.0265	382	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_003688285.1	s__Rhodophyticola porphyridii	77.8352	338	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.7876	306	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	77.6645	292	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.5168	323	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009649175.1	s__Rhodovulum strictum	77.3771	285	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:26,416] [INFO] GTDB search result was written to OceanDNA-b29554/result_gtdb.tsv
[2023-03-18 23:45:26,416] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:26,418] [INFO] DFAST_QC result json was written to OceanDNA-b29554/dqc_result.json
[2023-03-18 23:45:26,418] [INFO] DFAST_QC completed!
[2023-03-18 23:45:26,419] [INFO] Total running time: 0h1m20s