[2023-03-17 22:53:09,078] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:53:09,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:53:09,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference
[2023-03-17 22:53:12,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:53:12,179] [INFO] Task started: Prodigal
[2023-03-17 22:53:12,179] [INFO] Running command: cat /var/lib/cwl/stga1b216f4-5ea0-4b43-b355-4b7a5a362985/OceanDNA-b30166.fa | prodigal -d OceanDNA-b30166/cds.fna -a OceanDNA-b30166/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:53:28,918] [INFO] Task succeeded: Prodigal
[2023-03-17 22:53:28,918] [INFO] Task started: HMMsearch
[2023-03-17 22:53:28,918] [INFO] Running command: hmmsearch --tblout OceanDNA-b30166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference/reference_markers.hmm OceanDNA-b30166/protein.faa > /dev/null
[2023-03-17 22:53:29,112] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:53:29,112] [INFO] Found 6/6 markers.
[2023-03-17 22:53:29,130] [INFO] Query marker FASTA was written to OceanDNA-b30166/markers.fasta
[2023-03-17 22:53:29,131] [INFO] Task started: Blastn
[2023-03-17 22:53:29,131] [INFO] Running command: blastn -query OceanDNA-b30166/markers.fasta -db /var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference/reference_markers.fasta -out OceanDNA-b30166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:53:29,814] [INFO] Task succeeded: Blastn
[2023-03-17 22:53:29,815] [INFO] Selected 21 target genomes.
[2023-03-17 22:53:29,815] [INFO] Target genome list was writen to OceanDNA-b30166/target_genomes.txt
[2023-03-17 22:53:29,824] [INFO] Task started: fastANI
[2023-03-17 22:53:29,824] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b216f4-5ea0-4b43-b355-4b7a5a362985/OceanDNA-b30166.fa --refList OceanDNA-b30166/target_genomes.txt --output OceanDNA-b30166/fastani_result.tsv --threads 1
[2023-03-17 22:53:44,151] [INFO] Task succeeded: fastANI
[2023-03-17 22:53:44,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:53:44,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:53:44,165] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:53:44,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:53:44,165] [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
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	78.7343	511	859	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	78.5163	400	859	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	78.5127	401	859	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	78.4529	412	859	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.587	264	859	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.4833	235	859	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.3884	240	859	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.3861	288	859	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.3828	242	859	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.3492	279	859	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.3266	236	859	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.2861	280	859	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.2157	240	859	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.9638	259	859	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.473	157	859	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	76.3349	128	859	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	76.3345	128	859	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.3159	85	859	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.3141	103	859	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.2989	111	859	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.0397	97	859	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:53:44,166] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30166/tc_result.tsv
[2023-03-17 22:53:44,166] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:53:44,166] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:53:44,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference/checkm_data
[2023-03-17 22:53:44,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:53:44,172] [INFO] Task started: CheckM
[2023-03-17 22:53:44,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30166/checkm_input OceanDNA-b30166/checkm_result
[2023-03-17 22:54:27,737] [INFO] Task succeeded: CheckM
[2023-03-17 22:54:27,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:54:27,741] [INFO] ===== Completeness check finished =====
[2023-03-17 22:54:27,741] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:54:27,741] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30166/markers.fasta)
[2023-03-17 22:54:27,742] [INFO] Task started: Blastn
[2023-03-17 22:54:27,742] [INFO] Running command: blastn -query OceanDNA-b30166/markers.fasta -db /var/lib/cwl/stg934b5572-0809-4264-8340-7489574ddd37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:29,090] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:29,091] [INFO] Selected 20 target genomes.
[2023-03-17 22:54:29,091] [INFO] Target genome list was writen to OceanDNA-b30166/target_genomes_gtdb.txt
[2023-03-17 22:54:29,109] [INFO] Task started: fastANI
[2023-03-17 22:54:29,109] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b216f4-5ea0-4b43-b355-4b7a5a362985/OceanDNA-b30166.fa --refList OceanDNA-b30166/target_genomes_gtdb.txt --output OceanDNA-b30166/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:54:43,400] [INFO] Task succeeded: fastANI
[2023-03-17 22:54:43,412] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:54:43,412] [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_003610455.1	s__Sulfitobacter guttiformis	78.7302	512	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196805.1	s__Sulfitobacter undariae	78.5163	400	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	78.4629	411	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018200035.1	s__Sulfitobacter sp018200035	78.0308	411	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.5903	265	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.5775	320	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.3828	242	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.3266	236	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.2951	276	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	77.2907	288	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.2861	280	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.259	211	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.2037	244	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352085.1	s__Sulfitobacter sp003352085	77.0297	218	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	76.9731	258	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	76.877	224	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	76.4873	128	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	76.473	157	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	76.3669	148	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	76.3638	137	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:54:43,413] [INFO] GTDB search result was written to OceanDNA-b30166/result_gtdb.tsv
[2023-03-17 22:54:43,413] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:54:43,416] [INFO] DFAST_QC result json was written to OceanDNA-b30166/dqc_result.json
[2023-03-17 22:54:43,416] [INFO] DFAST_QC completed!
[2023-03-17 22:54:43,416] [INFO] Total running time: 0h1m34s