[2023-03-15 18:39:13,540] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:13,540] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:13,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference
[2023-03-15 18:39:15,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:15,276] [INFO] Task started: Prodigal
[2023-03-15 18:39:15,276] [INFO] Running command: cat /var/lib/cwl/stg2793fcdd-8ed3-4bc2-a611-5097223002eb/OceanDNA-b30120.fa | prodigal -d OceanDNA-b30120/cds.fna -a OceanDNA-b30120/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:40,546] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:40,547] [INFO] Task started: HMMsearch
[2023-03-15 18:39:40,547] [INFO] Running command: hmmsearch --tblout OceanDNA-b30120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference/reference_markers.hmm OceanDNA-b30120/protein.faa > /dev/null
[2023-03-15 18:39:40,751] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:40,751] [INFO] Found 6/6 markers.
[2023-03-15 18:39:40,778] [INFO] Query marker FASTA was written to OceanDNA-b30120/markers.fasta
[2023-03-15 18:39:40,779] [INFO] Task started: Blastn
[2023-03-15 18:39:40,779] [INFO] Running command: blastn -query OceanDNA-b30120/markers.fasta -db /var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference/reference_markers.fasta -out OceanDNA-b30120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:41,636] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:41,637] [INFO] Selected 19 target genomes.
[2023-03-15 18:39:41,637] [INFO] Target genome list was writen to OceanDNA-b30120/target_genomes.txt
[2023-03-15 18:39:41,653] [INFO] Task started: fastANI
[2023-03-15 18:39:41,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg2793fcdd-8ed3-4bc2-a611-5097223002eb/OceanDNA-b30120.fa --refList OceanDNA-b30120/target_genomes.txt --output OceanDNA-b30120/fastani_result.tsv --threads 1
[2023-03-15 18:39:57,375] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:57,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:57,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:57,387] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:57,387] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:39:57,387] [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
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	87.8913	1113	1278	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	80.6811	697	1278	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	80.6095	696	1278	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	79.4722	648	1278	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	79.4597	668	1278	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	79.4557	642	1278	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.6678	493	1278	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.3753	473	1278	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.3477	480	1278	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.9259	407	1278	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.7309	383	1278	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.6483	346	1278	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.3858	283	1278	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.2899	292	1278	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.0104	246	1278	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9396	256	1278	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	76.8531	262	1278	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.7085	232	1278	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6772	240	1278	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:39:57,387] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30120/tc_result.tsv
[2023-03-15 18:39:57,388] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:57,388] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:57,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference/checkm_data
[2023-03-15 18:39:57,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:57,398] [INFO] Task started: CheckM
[2023-03-15 18:39:57,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30120/checkm_input OceanDNA-b30120/checkm_result
[2023-03-15 18:41:00,933] [INFO] Task succeeded: CheckM
[2023-03-15 18:41:00,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:41:00,936] [INFO] ===== Completeness check finished =====
[2023-03-15 18:41:00,936] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:41:00,936] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30120/markers.fasta)
[2023-03-15 18:41:00,938] [INFO] Task started: Blastn
[2023-03-15 18:41:00,938] [INFO] Running command: blastn -query OceanDNA-b30120/markers.fasta -db /var/lib/cwl/stg3fca6f3f-812c-47b9-b879-b2b212db344c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:41:02,608] [INFO] Task succeeded: Blastn
[2023-03-15 18:41:02,609] [INFO] Selected 7 target genomes.
[2023-03-15 18:41:02,609] [INFO] Target genome list was writen to OceanDNA-b30120/target_genomes_gtdb.txt
[2023-03-15 18:41:02,806] [INFO] Task started: fastANI
[2023-03-15 18:41:02,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg2793fcdd-8ed3-4bc2-a611-5097223002eb/OceanDNA-b30120.fa --refList OceanDNA-b30120/target_genomes_gtdb.txt --output OceanDNA-b30120/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:41:10,100] [INFO] Task succeeded: fastANI
[2023-03-15 18:41:10,105] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:41:10,105] [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_002080415.1	s__Roseovarius mucosus_A	98.3388	1243	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	conclusive
GCA_018066915.1	s__Roseovarius sp018066915	88.1483	932	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_000768555.3	s__Roseovarius mucosus	87.895	1113	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	-
GCF_000152845.1	s__Roseovarius sp000152845	85.7599	1016	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.99	97.99	0.83	0.83	2	-
GCF_000744325.1	s__Roseovarius sp000744325	83.6146	925	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	80.69	696	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	78.8465	424	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-15 18:41:10,105] [INFO] GTDB search result was written to OceanDNA-b30120/result_gtdb.tsv
[2023-03-15 18:41:10,105] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:41:10,107] [INFO] DFAST_QC result json was written to OceanDNA-b30120/dqc_result.json
[2023-03-15 18:41:10,107] [INFO] DFAST_QC completed!
[2023-03-15 18:41:10,107] [INFO] Total running time: 0h1m57s