[2023-03-15 16:25:57,980] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,980] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference
[2023-03-15 16:26:01,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:26:01,658] [INFO] Task started: Prodigal
[2023-03-15 16:26:01,658] [INFO] Running command: cat /var/lib/cwl/stgd882983e-15fe-4b81-b143-34bfb076503d/OceanDNA-b30169.fa | prodigal -d OceanDNA-b30169/cds.fna -a OceanDNA-b30169/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:26,072] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:26,073] [INFO] Task started: HMMsearch
[2023-03-15 16:26:26,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b30169/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference/reference_markers.hmm OceanDNA-b30169/protein.faa > /dev/null
[2023-03-15 16:26:26,289] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:26,289] [INFO] Found 6/6 markers.
[2023-03-15 16:26:26,320] [INFO] Query marker FASTA was written to OceanDNA-b30169/markers.fasta
[2023-03-15 16:26:26,321] [INFO] Task started: Blastn
[2023-03-15 16:26:26,321] [INFO] Running command: blastn -query OceanDNA-b30169/markers.fasta -db /var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference/reference_markers.fasta -out OceanDNA-b30169/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:27,067] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:27,075] [INFO] Selected 20 target genomes.
[2023-03-15 16:26:27,076] [INFO] Target genome list was writen to OceanDNA-b30169/target_genomes.txt
[2023-03-15 16:26:27,090] [INFO] Task started: fastANI
[2023-03-15 16:26:27,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgd882983e-15fe-4b81-b143-34bfb076503d/OceanDNA-b30169.fa --refList OceanDNA-b30169/target_genomes.txt --output OceanDNA-b30169/fastani_result.tsv --threads 1
[2023-03-15 16:26:42,042] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:42,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:42,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:42,054] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:42,054] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:26:42,055] [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 mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.3691	549	1230	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	78.2851	497	1230	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.2317	506	1230	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	78.2289	502	1230	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.988	435	1230	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.9873	409	1230	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.9711	406	1230	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.8599	361	1230	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.6996	421	1230	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.6867	418	1230	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.6763	343	1230	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.6251	426	1230	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.5961	357	1230	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.4795	400	1230	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.758	168	1230	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.6615	204	1230	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.5043	173	1230	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.3977	182	1230	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.3865	183	1230	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.3064	190	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:26:42,056] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30169/tc_result.tsv
[2023-03-15 16:26:42,058] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:42,058] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:42,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference/checkm_data
[2023-03-15 16:26:42,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:42,072] [INFO] Task started: CheckM
[2023-03-15 16:26:42,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30169/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30169/checkm_input OceanDNA-b30169/checkm_result
[2023-03-15 16:27:44,658] [INFO] Task succeeded: CheckM
[2023-03-15 16:27:44,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:27:44,694] [INFO] ===== Completeness check finished =====
[2023-03-15 16:27:44,694] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:27:44,694] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30169/markers.fasta)
[2023-03-15 16:27:44,696] [INFO] Task started: Blastn
[2023-03-15 16:27:44,696] [INFO] Running command: blastn -query OceanDNA-b30169/markers.fasta -db /var/lib/cwl/stg85b8daa9-d9e1-49fe-86a9-aefc85560b37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30169/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:27:46,110] [INFO] Task succeeded: Blastn
[2023-03-15 16:27:46,119] [INFO] Selected 19 target genomes.
[2023-03-15 16:27:46,119] [INFO] Target genome list was writen to OceanDNA-b30169/target_genomes_gtdb.txt
[2023-03-15 16:27:46,136] [INFO] Task started: fastANI
[2023-03-15 16:27:46,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgd882983e-15fe-4b81-b143-34bfb076503d/OceanDNA-b30169.fa --refList OceanDNA-b30169/target_genomes_gtdb.txt --output OceanDNA-b30169/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:28:02,916] [INFO] Task succeeded: fastANI
[2023-03-15 16:28:02,926] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:28:02,927] [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_001650875.1	s__Sulfitobacter sp001650875	78.7255	559	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.6883	553	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.5399	584	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	78.2851	497	1230	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	78.2803	553	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_000622325.1	s__Sulfitobacter geojensis	78.2216	503	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.0027	395	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.988	435	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.9681	407	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.889	429	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	77.8599	361	1230	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	77.6946	417	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_013002405.1	s__Sulfitobacter sp013002405	77.6866	458	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	77.6621	382	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.6328	425	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	77.4872	399	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.335	344	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.5879	274	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_004339675.1	s__Rhodovulum steppense	76.5043	173	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:28:02,929] [INFO] GTDB search result was written to OceanDNA-b30169/result_gtdb.tsv
[2023-03-15 16:28:02,931] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:28:02,936] [INFO] DFAST_QC result json was written to OceanDNA-b30169/dqc_result.json
[2023-03-15 16:28:02,936] [INFO] DFAST_QC completed!
[2023-03-15 16:28:02,936] [INFO] Total running time: 0h2m5s