[2023-03-15 18:12:37,904] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:12:37,904] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:12:37,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference
[2023-03-15 18:12:39,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:12:39,785] [INFO] Task started: Prodigal
[2023-03-15 18:12:39,786] [INFO] Running command: cat /var/lib/cwl/stg7b82095c-b629-4f81-98a8-3312422175b2/OceanDNA-b28010.fa | prodigal -d OceanDNA-b28010/cds.fna -a OceanDNA-b28010/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:13:08,539] [INFO] Task succeeded: Prodigal
[2023-03-15 18:13:08,539] [INFO] Task started: HMMsearch
[2023-03-15 18:13:08,540] [INFO] Running command: hmmsearch --tblout OceanDNA-b28010/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference/reference_markers.hmm OceanDNA-b28010/protein.faa > /dev/null
[2023-03-15 18:13:08,747] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:13:08,748] [INFO] Found 6/6 markers.
[2023-03-15 18:13:08,773] [INFO] Query marker FASTA was written to OceanDNA-b28010/markers.fasta
[2023-03-15 18:13:08,773] [INFO] Task started: Blastn
[2023-03-15 18:13:08,773] [INFO] Running command: blastn -query OceanDNA-b28010/markers.fasta -db /var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference/reference_markers.fasta -out OceanDNA-b28010/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:13:09,482] [INFO] Task succeeded: Blastn
[2023-03-15 18:13:09,483] [INFO] Selected 21 target genomes.
[2023-03-15 18:13:09,483] [INFO] Target genome list was writen to OceanDNA-b28010/target_genomes.txt
[2023-03-15 18:13:09,597] [INFO] Task started: fastANI
[2023-03-15 18:13:09,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b82095c-b629-4f81-98a8-3312422175b2/OceanDNA-b28010.fa --refList OceanDNA-b28010/target_genomes.txt --output OceanDNA-b28010/fastani_result.tsv --threads 1
[2023-03-15 18:13:26,970] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:26,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:13:26,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:13:26,983] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:13:26,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:13:26,983] [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
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	80.8222	959	1479	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	80.8201	942	1479	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	80.7731	958	1479	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2726	506	1479	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	78.0892	435	1479	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.0099	437	1479	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	78.0026	437	1479	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	77.9709	438	1479	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8428	346	1479	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.8243	403	1479	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	77.7825	370	1479	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.719	446	1479	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.4288	296	1479	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.3864	378	1479	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.3143	323	1479	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	77.2505	323	1479	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.2032	223	1479	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	77.1091	226	1479	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.0254	180	1479	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.9759	199	1479	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.893	268	1479	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:13:26,983] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28010/tc_result.tsv
[2023-03-15 18:13:26,983] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:13:26,983] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:13:26,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference/checkm_data
[2023-03-15 18:13:26,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:13:26,993] [INFO] Task started: CheckM
[2023-03-15 18:13:26,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28010/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28010/checkm_input OceanDNA-b28010/checkm_result
[2023-03-15 18:14:38,688] [INFO] Task succeeded: CheckM
[2023-03-15 18:14:38,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:14:38,691] [INFO] ===== Completeness check finished =====
[2023-03-15 18:14:38,691] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:14:38,691] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28010/markers.fasta)
[2023-03-15 18:14:38,692] [INFO] Task started: Blastn
[2023-03-15 18:14:38,692] [INFO] Running command: blastn -query OceanDNA-b28010/markers.fasta -db /var/lib/cwl/stg9eac5ed0-6c72-4ecd-8773-0ff78ac3b7f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28010/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:14:39,838] [INFO] Task succeeded: Blastn
[2023-03-15 18:14:39,838] [INFO] Selected 11 target genomes.
[2023-03-15 18:14:39,838] [INFO] Target genome list was writen to OceanDNA-b28010/target_genomes_gtdb.txt
[2023-03-15 18:14:40,113] [INFO] Task started: fastANI
[2023-03-15 18:14:40,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b82095c-b629-4f81-98a8-3312422175b2/OceanDNA-b28010.fa --refList OceanDNA-b28010/target_genomes_gtdb.txt --output OceanDNA-b28010/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:14:51,939] [INFO] Task succeeded: fastANI
[2023-03-15 18:14:51,948] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:14:51,949] [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_002237555.1	s__Antarctobacter heliothermus_B	97.4922	1433	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	conclusive
GCF_900188425.1	s__Antarctobacter heliothermus	88.9702	1210	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218285.1	s__DP3N28-2 sp019218285	80.8294	941	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	80.8261	958	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900184945.1	s__Maliponia aquimaris	80.4314	893	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	79.2255	588	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017255395.1	s__AWRV01 sp017255395	79.1885	649	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	79.0798	664	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	78.2617	553	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.1538	491	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	77.6494	371	1479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:14:51,949] [INFO] GTDB search result was written to OceanDNA-b28010/result_gtdb.tsv
[2023-03-15 18:14:51,949] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:14:51,951] [INFO] DFAST_QC result json was written to OceanDNA-b28010/dqc_result.json
[2023-03-15 18:14:51,951] [INFO] DFAST_QC completed!
[2023-03-15 18:14:51,951] [INFO] Total running time: 0h2m14s