[2023-03-14 11:17:27,732] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:27,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:27,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference
[2023-03-14 11:17:28,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:28,870] [INFO] Task started: Prodigal
[2023-03-14 11:17:28,871] [INFO] Running command: cat /var/lib/cwl/stgf20f9bf0-3fd2-4965-92cd-a3fe1010fd71/OceanDNA-b16110.fa | prodigal -d OceanDNA-b16110/cds.fna -a OceanDNA-b16110/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:18:08,262] [INFO] Task succeeded: Prodigal
[2023-03-14 11:18:08,262] [INFO] Task started: HMMsearch
[2023-03-14 11:18:08,262] [INFO] Running command: hmmsearch --tblout OceanDNA-b16110/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference/reference_markers.hmm OceanDNA-b16110/protein.faa > /dev/null
[2023-03-14 11:18:08,565] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:18:08,565] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf20f9bf0-3fd2-4965-92cd-a3fe1010fd71/OceanDNA-b16110.fa]
[2023-03-14 11:18:08,612] [INFO] Query marker FASTA was written to OceanDNA-b16110/markers.fasta
[2023-03-14 11:18:08,613] [INFO] Task started: Blastn
[2023-03-14 11:18:08,614] [INFO] Running command: blastn -query OceanDNA-b16110/markers.fasta -db /var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference/reference_markers.fasta -out OceanDNA-b16110/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:18:09,132] [INFO] Task succeeded: Blastn
[2023-03-14 11:18:09,134] [INFO] Selected 22 target genomes.
[2023-03-14 11:18:09,134] [INFO] Target genome list was writen to OceanDNA-b16110/target_genomes.txt
[2023-03-14 11:18:09,150] [INFO] Task started: fastANI
[2023-03-14 11:18:09,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgf20f9bf0-3fd2-4965-92cd-a3fe1010fd71/OceanDNA-b16110.fa --refList OceanDNA-b16110/target_genomes.txt --output OceanDNA-b16110/fastani_result.tsv --threads 1
[2023-03-14 11:18:29,928] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:29,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:18:29,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:18:29,936] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:18:29,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:18:29,936] [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
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	76.0736	216	2343	95	below_threshold
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	75.6941	112	2343	95	below_threshold
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	75.6622	111	2343	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	75.5348	103	2343	95	below_threshold
Spirulina major	strain=PCC 6313	GCA_001890765.1	270636	270636	type	True	75.3739	66	2343	95	below_threshold
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	75.2346	80	2343	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	75.2321	85	2343	95	below_threshold
Acaryochloris marina	strain=MBIC11017	GCA_000018105.1	155978	155978	type	True	75.1708	50	2343	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	75.1563	57	2343	95	below_threshold
Leptothermofonsia sichuanensis	strain=PKUAC-SCTE412	GCA_019891175.1	2917832	2917832	type	True	75.1072	52	2343	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.0689	86	2343	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	75.0374	90	2343	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:18:29,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16110/tc_result.tsv
[2023-03-14 11:18:29,938] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:18:29,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:18:29,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference/checkm_data
[2023-03-14 11:18:29,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:18:29,949] [INFO] Task started: CheckM
[2023-03-14 11:18:29,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16110/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16110/checkm_input OceanDNA-b16110/checkm_result
[2023-03-14 11:20:03,193] [INFO] Task succeeded: CheckM
[2023-03-14 11:20:03,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:20:03,214] [INFO] ===== Completeness check finished =====
[2023-03-14 11:20:03,214] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:20:03,214] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16110/markers.fasta)
[2023-03-14 11:20:03,216] [INFO] Task started: Blastn
[2023-03-14 11:20:03,216] [INFO] Running command: blastn -query OceanDNA-b16110/markers.fasta -db /var/lib/cwl/stg8640edcc-8ce8-48f4-8964-21bf70b73f65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16110/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:20:03,914] [INFO] Task succeeded: Blastn
[2023-03-14 11:20:03,918] [INFO] Selected 21 target genomes.
[2023-03-14 11:20:03,918] [INFO] Target genome list was writen to OceanDNA-b16110/target_genomes_gtdb.txt
[2023-03-14 11:20:03,937] [INFO] Task started: fastANI
[2023-03-14 11:20:03,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgf20f9bf0-3fd2-4965-92cd-a3fe1010fd71/OceanDNA-b16110.fa --refList OceanDNA-b16110/target_genomes_gtdb.txt --output OceanDNA-b16110/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:20:30,286] [INFO] Task succeeded: fastANI
[2023-03-14 11:20:30,297] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:20:30,297] [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
GCA_011390955.1	s__Planktothricoides sp011390955	79.3654	1063	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276715.1	s__Planktothricoides sp001276715	79.2582	1004	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	99.30	99.29	0.94	0.94	3	-
GCA_001890975.1	s__Roseofilum reptotaenium_A	76.5841	133	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Roseofilum	95.0	97.72	97.70	0.90	0.89	3	-
GCA_010672085.1	s__Trichodesmium sp010672085	76.121	260	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317105.1	s__Oscillatoria acuminata	76.0857	212	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oscillatoria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313335.1	s__Phormidium pseudopriestleyi	75.9971	160	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Phormidium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331985.1	s__DSPX01 sp011331985	75.9499	172	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__DSPX01	95.0	99.98	99.98	0.96	0.96	2	-
GCF_016446395.1	s__DSPX01 sp016446395	75.8953	193	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__DSPX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695715.1	s__FACHB-68 sp014695715	75.7199	97	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__FACHB-68	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695725.1	s__FACHB-68 sp014695725	75.6298	86	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__FACHB-68	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746915.1	s__Desertifilum sp001746915	75.5362	109	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Desertifilum	95.0	99.94	99.93	0.99	0.98	4	-
GCF_900009135.1	s__Planktothrix sp900009135	75.4111	108	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890765.1	s__Spirulina major	75.3677	67	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005402965.1	s__Dolichospermum planctonicum	75.3254	61	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	98.27	96.37	0.91	0.88	5	-
GCA_012034055.1	s__JAAUSG01 sp012034055	75.2785	52	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JAAUSG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214075.1	s__Microcoleus vaginatus	75.2782	110	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695295.1	s__Microcoleus sp014695295	75.2716	107	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207155.1	s__Nodularia sp015207155	75.2423	80	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317225.1	s__Fischerella thermalis	75.1491	53	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	98.97	96.56	0.93	0.78	35	-
GCF_014698305.1	s__Anabaena lutea	75.0346	82	2343	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:20:30,299] [INFO] GTDB search result was written to OceanDNA-b16110/result_gtdb.tsv
[2023-03-14 11:20:30,302] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:20:30,306] [INFO] DFAST_QC result json was written to OceanDNA-b16110/dqc_result.json
[2023-03-14 11:20:30,306] [INFO] DFAST_QC completed!
[2023-03-14 11:20:30,306] [INFO] Total running time: 0h3m3s