[2023-06-28 13:31:21,429] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:21,431] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:21,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference
[2023-06-28 13:31:22,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:22,554] [INFO] Task started: Prodigal
[2023-06-28 13:31:22,555] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3571d09-d325-4dca-9051-cb587151aa02/GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:31:30,947] [INFO] Task succeeded: Prodigal
[2023-06-28 13:31:30,947] [INFO] Task started: HMMsearch
[2023-06-28 13:31:30,947] [INFO] Running command: hmmsearch --tblout GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference/reference_markers.hmm GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:31:31,142] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:31:31,143] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf3571d09-d325-4dca-9051-cb587151aa02/GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 13:31:31,177] [INFO] Query marker FASTA was written to GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 13:31:31,177] [INFO] Task started: Blastn
[2023-06-28 13:31:31,177] [INFO] Running command: blastn -query GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference/reference_markers.fasta -out GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:31,769] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:31,772] [INFO] Selected 14 target genomes.
[2023-06-28 13:31:31,773] [INFO] Target genome list was writen to GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 13:31:31,809] [INFO] Task started: fastANI
[2023-06-28 13:31:31,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3571d09-d325-4dca-9051-cb587151aa02/GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:31:42,290] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:42,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:31:42,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:31:42,301] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:31:42,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:31:42,301] [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
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	80.2575	440	889	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	80.1304	454	889	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	80.1022	463	889	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.8162	417	889	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	79.7703	420	889	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.2421	295	889	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.2316	299	889	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.2288	311	889	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.7509	259	889	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.5058	250	889	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.0456	158	889	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.8948	154	889	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.7544	165	889	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.5417	184	889	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:31:42,303] [INFO] DFAST Taxonomy check result was written to GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 13:31:42,303] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:31:42,303] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:31:42,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference/checkm_data
[2023-06-28 13:31:42,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:31:42,346] [INFO] Task started: CheckM
[2023-06-28 13:31:42,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 13:32:09,572] [INFO] Task succeeded: CheckM
[2023-06-28 13:32:09,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:32:09,593] [INFO] ===== Completeness check finished =====
[2023-06-28 13:32:09,594] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:32:09,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 13:32:09,595] [INFO] Task started: Blastn
[2023-06-28 13:32:09,595] [INFO] Running command: blastn -query GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81159403-8e5d-452a-b2b6-9b2f56679239/dqc_reference/reference_markers_gtdb.fasta -out GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:10,495] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:10,499] [INFO] Selected 12 target genomes.
[2023-06-28 13:32:10,500] [INFO] Target genome list was writen to GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:32:10,516] [INFO] Task started: fastANI
[2023-06-28 13:32:10,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3571d09-d325-4dca-9051-cb587151aa02/GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:32:20,534] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:20,543] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:32:20,543] [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_900143635.1	s__FREY01 sp900143635	82.245	609	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__FREY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	80.2842	438	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_001458395.1	s__Leisingera aquaemixtae	80.1498	452	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000473325.1	s__Leisingera caerulea	80.072	465	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	80.0599	459	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_013317235.1	s__Leisingera sp013317235	80.0338	460	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	79.9187	455	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	79.8625	466	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	79.7903	419	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	78.2412	295	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_002407245.1	s__Phaeobacter piscinae	78.2329	310	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCA_002162795.1	s__Parasedimentitalea sp002162795	77.372	237	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:32:20,545] [INFO] GTDB search result was written to GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 13:32:20,545] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:32:20,550] [INFO] DFAST_QC result json was written to GCA_913054485.1_SRR3646399_bin.4_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 13:32:20,550] [INFO] DFAST_QC completed!
[2023-06-28 13:32:20,550] [INFO] Total running time: 0h0m59s