[2023-03-15 21:48:07,253] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,263] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference
[2023-03-15 21:48:08,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,884] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,884] [INFO] Running command: cat /var/lib/cwl/stga6d523be-c833-4f83-822b-e4be5be9ff8b/OceanDNA-b35916.fa | prodigal -d OceanDNA-b35916/cds.fna -a OceanDNA-b35916/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:27,628] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:27,629] [INFO] Task started: HMMsearch
[2023-03-15 21:48:27,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b35916/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference/reference_markers.hmm OceanDNA-b35916/protein.faa > /dev/null
[2023-03-15 21:48:27,823] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:27,823] [INFO] Found 6/6 markers.
[2023-03-15 21:48:27,844] [INFO] Query marker FASTA was written to OceanDNA-b35916/markers.fasta
[2023-03-15 21:48:27,845] [INFO] Task started: Blastn
[2023-03-15 21:48:27,845] [INFO] Running command: blastn -query OceanDNA-b35916/markers.fasta -db /var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference/reference_markers.fasta -out OceanDNA-b35916/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:28,579] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:28,579] [INFO] Selected 21 target genomes.
[2023-03-15 21:48:28,580] [INFO] Target genome list was writen to OceanDNA-b35916/target_genomes.txt
[2023-03-15 21:48:28,616] [INFO] Task started: fastANI
[2023-03-15 21:48:28,616] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d523be-c833-4f83-822b-e4be5be9ff8b/OceanDNA-b35916.fa --refList OceanDNA-b35916/target_genomes.txt --output OceanDNA-b35916/fastani_result.tsv --threads 1
[2023-03-15 21:48:42,624] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:42,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:42,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:42,637] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:42,637] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:42,637] [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
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	87.4738	802	976	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	76.6075	160	976	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5794	156	976	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.5397	143	976	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4597	147	976	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.4283	131	976	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.3939	131	976	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	76.3878	136	976	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.3083	150	976	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.2964	151	976	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.2792	124	976	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.2308	99	976	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.1817	143	976	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	76.1745	127	976	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	76.1675	130	976	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.0362	97	976	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.0129	173	976	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	75.9613	103	976	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.9172	228	976	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:42,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35916/tc_result.tsv
[2023-03-15 21:48:42,637] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:42,637] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:42,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference/checkm_data
[2023-03-15 21:48:42,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:42,643] [INFO] Task started: CheckM
[2023-03-15 21:48:42,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35916/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35916/checkm_input OceanDNA-b35916/checkm_result
[2023-03-15 21:49:33,678] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:33,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:33,681] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:33,681] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:33,681] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35916/markers.fasta)
[2023-03-15 21:49:33,682] [INFO] Task started: Blastn
[2023-03-15 21:49:33,682] [INFO] Running command: blastn -query OceanDNA-b35916/markers.fasta -db /var/lib/cwl/stg64825103-b8b4-423f-85f1-93d104f3d2d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35916/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:34,969] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:34,970] [INFO] Selected 18 target genomes.
[2023-03-15 21:49:34,970] [INFO] Target genome list was writen to OceanDNA-b35916/target_genomes_gtdb.txt
[2023-03-15 21:49:35,062] [INFO] Task started: fastANI
[2023-03-15 21:49:35,062] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d523be-c833-4f83-822b-e4be5be9ff8b/OceanDNA-b35916.fa --refList OceanDNA-b35916/target_genomes_gtdb.txt --output OceanDNA-b35916/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:44,375] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:44,385] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:49:44,385] [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_001697225.1	s__Immundisolibacter cernigliae	87.4429	804	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359565.1	s__Immundisolibacter sp014359565	86.9719	715	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526065.1	s__Immundisolibacter sp003526065	82.2328	439	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833355.1	s__Denitratisoma sp007833355	78.1694	140	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.7698	142	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.7399	120	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348725.1	s__GCA-013348725 sp013348725	76.667	135	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	76.6505	144	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.5255	176	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_007128895.1	s__SKWO01 sp007128895	76.5158	93	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SKWO01;f__SKWO01;g__SKWO01	95.0	99.65	99.65	0.89	0.89	2	-
GCA_003695825.1	s__J048 sp003695825	76.5125	86	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	76.4226	129	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCA_004322005.1	s__Rhodanobacter sp004322005	76.34	125	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192745.1	s__Luteimonas sp014192745	76.3163	130	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115705.1	s__Frateuria_A terrea	76.3083	150	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.3045	108	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329435.1	s__Rhodanobacter sp008329435	76.2831	119	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:49:44,385] [INFO] GTDB search result was written to OceanDNA-b35916/result_gtdb.tsv
[2023-03-15 21:49:44,385] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:44,387] [INFO] DFAST_QC result json was written to OceanDNA-b35916/dqc_result.json
[2023-03-15 21:49:44,387] [INFO] DFAST_QC completed!
[2023-03-15 21:49:44,387] [INFO] Total running time: 0h1m37s