[2023-03-16 20:59:00,652] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:59:00,652] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:59:00,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference
[2023-03-16 20:59:03,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:59:03,535] [INFO] Task started: Prodigal
[2023-03-16 20:59:03,549] [INFO] Running command: cat /var/lib/cwl/stg25fafd9e-3499-49df-93bb-2aced2ae6e4b/OceanDNA-b30007.fa | prodigal -d OceanDNA-b30007/cds.fna -a OceanDNA-b30007/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:59:30,242] [INFO] Task succeeded: Prodigal
[2023-03-16 20:59:30,242] [INFO] Task started: HMMsearch
[2023-03-16 20:59:30,242] [INFO] Running command: hmmsearch --tblout OceanDNA-b30007/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference/reference_markers.hmm OceanDNA-b30007/protein.faa > /dev/null
[2023-03-16 20:59:30,452] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:59:30,453] [INFO] Found 6/6 markers.
[2023-03-16 20:59:30,474] [INFO] Query marker FASTA was written to OceanDNA-b30007/markers.fasta
[2023-03-16 20:59:30,475] [INFO] Task started: Blastn
[2023-03-16 20:59:30,475] [INFO] Running command: blastn -query OceanDNA-b30007/markers.fasta -db /var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference/reference_markers.fasta -out OceanDNA-b30007/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:59:31,378] [INFO] Task succeeded: Blastn
[2023-03-16 20:59:31,379] [INFO] Selected 21 target genomes.
[2023-03-16 20:59:31,379] [INFO] Target genome list was writen to OceanDNA-b30007/target_genomes.txt
[2023-03-16 20:59:31,390] [INFO] Task started: fastANI
[2023-03-16 20:59:31,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg25fafd9e-3499-49df-93bb-2aced2ae6e4b/OceanDNA-b30007.fa --refList OceanDNA-b30007/target_genomes.txt --output OceanDNA-b30007/fastani_result.tsv --threads 1
[2023-03-16 20:59:49,235] [INFO] Task succeeded: fastANI
[2023-03-16 20:59:49,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:59:49,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:59:49,247] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 20:59:49,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 20:59:49,248] [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
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	95.2388	1071	1200	95	conclusive
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	95.1851	1069	1200	95	conclusive
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.3014	564	1200	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.2226	547	1200	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.1875	531	1200	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.1866	527	1200	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.1358	555	1200	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.0997	559	1200	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.0398	511	1200	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.0122	504	1200	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.9594	541	1200	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.9533	518	1200	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.2763	412	1200	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	78.2369	457	1200	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.2143	410	1200	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1706	377	1200	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.1677	433	1200	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.6584	304	1200	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	77.5516	460	1200	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.5302	318	1200	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4506	302	1200	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:59:49,248] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30007/tc_result.tsv
[2023-03-16 20:59:49,248] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:59:49,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:59:49,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference/checkm_data
[2023-03-16 20:59:49,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:59:49,254] [INFO] Task started: CheckM
[2023-03-16 20:59:49,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30007/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30007/checkm_input OceanDNA-b30007/checkm_result
[2023-03-16 21:00:56,774] [INFO] Task succeeded: CheckM
[2023-03-16 21:00:56,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:00:56,777] [INFO] ===== Completeness check finished =====
[2023-03-16 21:00:56,777] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:00:56,777] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30007/markers.fasta)
[2023-03-16 21:00:56,777] [INFO] Task started: Blastn
[2023-03-16 21:00:56,777] [INFO] Running command: blastn -query OceanDNA-b30007/markers.fasta -db /var/lib/cwl/stg64ccf1a7-5ccb-468c-a74b-f34325b1bb65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30007/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:00:58,525] [INFO] Task succeeded: Blastn
[2023-03-16 21:00:58,526] [INFO] Selected 26 target genomes.
[2023-03-16 21:00:58,526] [INFO] Target genome list was writen to OceanDNA-b30007/target_genomes_gtdb.txt
[2023-03-16 21:00:58,759] [INFO] Task started: fastANI
[2023-03-16 21:00:58,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg25fafd9e-3499-49df-93bb-2aced2ae6e4b/OceanDNA-b30007.fa --refList OceanDNA-b30007/target_genomes_gtdb.txt --output OceanDNA-b30007/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:01:29,053] [INFO] Task succeeded: fastANI
[2023-03-16 21:01:29,068] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:01:29,068] [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_000688295.1	s__Pseudooceanicola nanhaiensis	95.2388	1071	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002210105.1	s__Pseudooceanicola sp002210105	81.9375	780	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	81.0193	477	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	79.8643	581	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	79.4534	578	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	79.3384	550	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959925.1	s__Pseudooceanicola onchidii	79.2012	528	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.1693	496	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	79.1247	512	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.1168	541	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900102075.1	s__Salipiger thiooxidans	79.1138	558	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_002300555.1	s__Salipiger sp002300555	79.0833	415	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	79.0765	506	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.9961	461	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	78.9581	510	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.853	458	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112685.1	s__Roseivivax sediminis	78.823	464	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.7073	495	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCA_015689685.1	s__HKCCE3408 sp015689685	78.4815	466	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.4546	450	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	78.4424	442	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	78.2763	412	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	78.14	407	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	78.016	420	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113695.1	s__Albimonas pacifica	77.5735	456	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	76.6927	198	1200	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:01:29,068] [INFO] GTDB search result was written to OceanDNA-b30007/result_gtdb.tsv
[2023-03-16 21:01:29,068] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:01:29,071] [INFO] DFAST_QC result json was written to OceanDNA-b30007/dqc_result.json
[2023-03-16 21:01:29,071] [INFO] DFAST_QC completed!
[2023-03-16 21:01:29,071] [INFO] Total running time: 0h2m28s