[2023-03-18 07:58:06,158] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:58:06,158] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:58:06,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference
[2023-03-18 07:58:07,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:58:07,258] [INFO] Task started: Prodigal
[2023-03-18 07:58:07,258] [INFO] Running command: cat /var/lib/cwl/stg2a78be59-d6ce-461a-87bc-6df4f9cc3c65/OceanDNA-b22481.fa | prodigal -d OceanDNA-b22481/cds.fna -a OceanDNA-b22481/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:58:28,070] [INFO] Task succeeded: Prodigal
[2023-03-18 07:58:28,071] [INFO] Task started: HMMsearch
[2023-03-18 07:58:28,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b22481/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference/reference_markers.hmm OceanDNA-b22481/protein.faa > /dev/null
[2023-03-18 07:58:28,300] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:58:28,301] [INFO] Found 6/6 markers.
[2023-03-18 07:58:28,325] [INFO] Query marker FASTA was written to OceanDNA-b22481/markers.fasta
[2023-03-18 07:58:28,325] [INFO] Task started: Blastn
[2023-03-18 07:58:28,325] [INFO] Running command: blastn -query OceanDNA-b22481/markers.fasta -db /var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference/reference_markers.fasta -out OceanDNA-b22481/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:58:28,870] [INFO] Task succeeded: Blastn
[2023-03-18 07:58:28,870] [INFO] Selected 33 target genomes.
[2023-03-18 07:58:28,871] [INFO] Target genome list was writen to OceanDNA-b22481/target_genomes.txt
[2023-03-18 07:58:28,886] [INFO] Task started: fastANI
[2023-03-18 07:58:28,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a78be59-d6ce-461a-87bc-6df4f9cc3c65/OceanDNA-b22481.fa --refList OceanDNA-b22481/target_genomes.txt --output OceanDNA-b22481/fastani_result.tsv --threads 1
[2023-03-18 07:59:03,605] [INFO] Task succeeded: fastANI
[2023-03-18 07:59:03,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:59:03,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:59:03,615] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:59:03,615] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:59:03,615] [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
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	75.9082	75	991	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	75.8745	81	991	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	75.8545	95	991	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	75.8468	50	991	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	75.8384	78	991	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.7792	93	991	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	75.7499	62	991	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	75.7078	88	991	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	75.6649	117	991	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	75.6407	75	991	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.5944	94	991	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.5798	91	991	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	75.5597	74	991	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	75.5318	75	991	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	75.4274	65	991	95	below_threshold
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	75.3309	66	991	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	74.5881	53	991	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:59:03,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22481/tc_result.tsv
[2023-03-18 07:59:03,615] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:59:03,616] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:59:03,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference/checkm_data
[2023-03-18 07:59:03,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:59:03,622] [INFO] Task started: CheckM
[2023-03-18 07:59:03,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22481/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22481/checkm_input OceanDNA-b22481/checkm_result
[2023-03-18 07:59:56,830] [INFO] Task succeeded: CheckM
[2023-03-18 07:59:56,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.98%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:59:56,834] [INFO] ===== Completeness check finished =====
[2023-03-18 07:59:56,834] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:59:56,834] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22481/markers.fasta)
[2023-03-18 07:59:56,834] [INFO] Task started: Blastn
[2023-03-18 07:59:56,834] [INFO] Running command: blastn -query OceanDNA-b22481/markers.fasta -db /var/lib/cwl/stg4f6c9ee5-560c-46ef-8c49-29c6c162cb7a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22481/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:59:57,916] [INFO] Task succeeded: Blastn
[2023-03-18 07:59:57,917] [INFO] Selected 28 target genomes.
[2023-03-18 07:59:57,917] [INFO] Target genome list was writen to OceanDNA-b22481/target_genomes_gtdb.txt
[2023-03-18 07:59:57,958] [INFO] Task started: fastANI
[2023-03-18 07:59:57,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a78be59-d6ce-461a-87bc-6df4f9cc3c65/OceanDNA-b22481.fa --refList OceanDNA-b22481/target_genomes_gtdb.txt --output OceanDNA-b22481/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:00:27,552] [INFO] Task succeeded: fastANI
[2023-03-18 08:00:27,563] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:00:27,563] [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_001027925.1	s__Rhodopirellula islandica	75.8908	80	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	75.8885	76	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	75.8545	95	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196115.1	s__Rhodopirellula baltica	75.8468	50	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_007752935.1	s__Crateriforma conspicua	75.7655	94	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_000338295.1	s__Rhodopirellula europaea	75.7499	62	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_007859915.1	s__Rhodopirellula pilleata	75.7202	92	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	75.7078	88	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	75.6573	74	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_008035925.1	s__Stieleria maiorica	75.6557	116	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	75.5944	94	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_002289565.1	s__Stieleria sp002289565	75.5861	112	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860045.1	s__Stieleria varia	75.5747	73	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	75.5549	93	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	75.5318	75	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	75.4686	120	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007751715.1	s__Rosistilla oblonga	75.4274	65	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	97.20	97.20	0.92	0.92	2	-
GCA_007741475.1	s__Rosistilla sp007741475	75.3309	66	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694185.1	s__UBA6163 sp007694185	75.2668	54	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	75.2483	57	991	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:00:27,563] [INFO] GTDB search result was written to OceanDNA-b22481/result_gtdb.tsv
[2023-03-18 08:00:27,563] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:00:27,565] [INFO] DFAST_QC result json was written to OceanDNA-b22481/dqc_result.json
[2023-03-18 08:00:27,565] [INFO] DFAST_QC completed!
[2023-03-18 08:00:27,565] [INFO] Total running time: 0h2m21s