[2023-03-15 05:43:38,962] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:43:38,963] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:43:38,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference
[2023-03-15 05:43:40,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:43:40,058] [INFO] Task started: Prodigal
[2023-03-15 05:43:40,058] [INFO] Running command: cat /var/lib/cwl/stg44ae5cdb-d988-46c2-9e05-f7d82235c021/OceanDNA-b30027.fa | prodigal -d OceanDNA-b30027/cds.fna -a OceanDNA-b30027/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:44:06,632] [INFO] Task succeeded: Prodigal
[2023-03-15 05:44:06,632] [INFO] Task started: HMMsearch
[2023-03-15 05:44:06,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b30027/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference/reference_markers.hmm OceanDNA-b30027/protein.faa > /dev/null
[2023-03-15 05:44:06,845] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:44:06,845] [INFO] Found 6/6 markers.
[2023-03-15 05:44:06,870] [INFO] Query marker FASTA was written to OceanDNA-b30027/markers.fasta
[2023-03-15 05:44:06,871] [INFO] Task started: Blastn
[2023-03-15 05:44:06,871] [INFO] Running command: blastn -query OceanDNA-b30027/markers.fasta -db /var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference/reference_markers.fasta -out OceanDNA-b30027/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:44:07,538] [INFO] Task succeeded: Blastn
[2023-03-15 05:44:07,539] [INFO] Selected 19 target genomes.
[2023-03-15 05:44:07,539] [INFO] Target genome list was writen to OceanDNA-b30027/target_genomes.txt
[2023-03-15 05:44:07,549] [INFO] Task started: fastANI
[2023-03-15 05:44:07,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ae5cdb-d988-46c2-9e05-f7d82235c021/OceanDNA-b30027.fa --refList OceanDNA-b30027/target_genomes.txt --output OceanDNA-b30027/fastani_result.tsv --threads 1
[2023-03-15 05:44:22,004] [INFO] Task succeeded: fastANI
[2023-03-15 05:44:22,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:44:22,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:44:22,016] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:44:22,016] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:44:22,017] [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
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	83.6695	1022	1388	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	80.9069	834	1388	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	80.8586	825	1388	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.2666	503	1388	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.2232	426	1388	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.2145	433	1388	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.186	496	1388	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.182	449	1388	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.1689	486	1388	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.1106	500	1388	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	78.0976	431	1388	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	78.0943	432	1388	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.0815	435	1388	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	78.0797	405	1388	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	77.5773	327	1388	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6529	146	1388	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.5239	117	1388	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.4127	130	1388	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.9744	122	1388	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:44:22,021] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30027/tc_result.tsv
[2023-03-15 05:44:22,027] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:44:22,027] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:44:22,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference/checkm_data
[2023-03-15 05:44:22,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:44:22,034] [INFO] Task started: CheckM
[2023-03-15 05:44:22,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30027/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30027/checkm_input OceanDNA-b30027/checkm_result
[2023-03-15 05:45:26,917] [INFO] Task succeeded: CheckM
[2023-03-15 05:45:26,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:45:26,944] [INFO] ===== Completeness check finished =====
[2023-03-15 05:45:26,944] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:45:26,944] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30027/markers.fasta)
[2023-03-15 05:45:26,945] [INFO] Task started: Blastn
[2023-03-15 05:45:26,945] [INFO] Running command: blastn -query OceanDNA-b30027/markers.fasta -db /var/lib/cwl/stg72d612b4-fa36-43ea-a60e-f9ee6e82e0fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30027/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:45:27,961] [INFO] Task succeeded: Blastn
[2023-03-15 05:45:27,962] [INFO] Selected 8 target genomes.
[2023-03-15 05:45:27,962] [INFO] Target genome list was writen to OceanDNA-b30027/target_genomes_gtdb.txt
[2023-03-15 05:45:27,970] [INFO] Task started: fastANI
[2023-03-15 05:45:27,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ae5cdb-d988-46c2-9e05-f7d82235c021/OceanDNA-b30027.fa --refList OceanDNA-b30027/target_genomes_gtdb.txt --output OceanDNA-b30027/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:45:36,371] [INFO] Task succeeded: fastANI
[2023-03-15 05:45:36,377] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:45:36,377] [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_000152965.1	s__Pseudophaeobacter sp000152965	98.3004	1282	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.26	98.26	0.93	0.93	2	conclusive
GCF_001294455.1	s__Pseudophaeobacter sp001294455	84.8475	1004	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.13	98.13	0.97	0.97	2	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	84.3443	1023	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	83.6541	1024	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479575.1	s__Pseudophaeobacter sp905479575	83.612	933	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	81.2105	837	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	78.2007	500	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_001258055.1	s__Phaeobacter italicus	78.0976	431	1388	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
--------------------------------------------------------------------------------
[2023-03-15 05:45:36,378] [INFO] GTDB search result was written to OceanDNA-b30027/result_gtdb.tsv
[2023-03-15 05:45:36,378] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:45:36,379] [INFO] DFAST_QC result json was written to OceanDNA-b30027/dqc_result.json
[2023-03-15 05:45:36,379] [INFO] DFAST_QC completed!
[2023-03-15 05:45:36,380] [INFO] Total running time: 0h1m57s