[2023-03-19 00:33:19,054] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,055] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference
[2023-03-19 00:33:20,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,245] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,245] [INFO] Running command: cat /var/lib/cwl/stg89ec39f7-e9b3-42d5-a7c6-d7cd249b737f/OceanDNA-b16201.fa | prodigal -d OceanDNA-b16201/cds.fna -a OceanDNA-b16201/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:48,289] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:48,290] [INFO] Task started: HMMsearch
[2023-03-19 00:33:48,290] [INFO] Running command: hmmsearch --tblout OceanDNA-b16201/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference/reference_markers.hmm OceanDNA-b16201/protein.faa > /dev/null
[2023-03-19 00:33:48,605] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:48,605] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89ec39f7-e9b3-42d5-a7c6-d7cd249b737f/OceanDNA-b16201.fa]
[2023-03-19 00:33:48,643] [INFO] Query marker FASTA was written to OceanDNA-b16201/markers.fasta
[2023-03-19 00:33:48,644] [INFO] Task started: Blastn
[2023-03-19 00:33:48,644] [INFO] Running command: blastn -query OceanDNA-b16201/markers.fasta -db /var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference/reference_markers.fasta -out OceanDNA-b16201/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:49,175] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:49,177] [INFO] Selected 25 target genomes.
[2023-03-19 00:33:49,178] [INFO] Target genome list was writen to OceanDNA-b16201/target_genomes.txt
[2023-03-19 00:33:49,198] [INFO] Task started: fastANI
[2023-03-19 00:33:49,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg89ec39f7-e9b3-42d5-a7c6-d7cd249b737f/OceanDNA-b16201.fa --refList OceanDNA-b16201/target_genomes.txt --output OceanDNA-b16201/fastani_result.tsv --threads 1
[2023-03-19 00:34:07,143] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:07,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:34:07,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:34:07,147] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:34:07,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:34:07,147] [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
Adonisia turfae	strain=CCMR0081	GCA_011009555.1	2950184	2950184	type	True	76.5997	226	1666	95	below_threshold
Halomicronema hongdechloris	strain=C2206	GCA_002075285.3	1209493	1209493	type	True	75.7658	92	1666	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:34:07,227] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16201/tc_result.tsv
[2023-03-19 00:34:07,228] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:34:07,228] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:34:07,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference/checkm_data
[2023-03-19 00:34:07,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:34:07,237] [INFO] Task started: CheckM
[2023-03-19 00:34:07,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16201/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16201/checkm_input OceanDNA-b16201/checkm_result
[2023-03-19 00:35:14,287] [INFO] Task succeeded: CheckM
[2023-03-19 00:35:14,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:35:14,303] [INFO] ===== Completeness check finished =====
[2023-03-19 00:35:14,303] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:35:14,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16201/markers.fasta)
[2023-03-19 00:35:14,304] [INFO] Task started: Blastn
[2023-03-19 00:35:14,304] [INFO] Running command: blastn -query OceanDNA-b16201/markers.fasta -db /var/lib/cwl/stg85210a72-0f73-42d4-8919-c305ceaf4f2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16201/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:35:15,047] [INFO] Task succeeded: Blastn
[2023-03-19 00:35:15,053] [INFO] Selected 24 target genomes.
[2023-03-19 00:35:15,053] [INFO] Target genome list was writen to OceanDNA-b16201/target_genomes_gtdb.txt
[2023-03-19 00:35:15,069] [INFO] Task started: fastANI
[2023-03-19 00:35:15,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg89ec39f7-e9b3-42d5-a7c6-d7cd249b737f/OceanDNA-b16201.fa --refList OceanDNA-b16201/target_genomes_gtdb.txt --output OceanDNA-b16201/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:35:33,218] [INFO] Task succeeded: fastANI
[2023-03-19 00:35:33,228] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:35:33,228] [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_018739885.1	s__Leptothoe spongobia	77.0729	166	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018739865.1	s__Leptothoe kymatousa	77.0339	225	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207065.1	s__Leptothoe ectocarpi	76.9179	309	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316115.1	s__Leptothoe sp000316115	76.8777	229	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482245.1	s__Leptothoe sp000482245	76.709	266	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011009555.1	s__Leptothoe sp011009555	76.6279	223	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	98.38	98.38	0.89	0.89	2	-
GCA_007694115.1	s__Nodosilinea sp007694115	76.3907	146	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763385.1	s__Nodosilinea sp000763385	76.3362	222	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016403105.1	s__Nodosilinea sp016403105	76.2995	127	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241845.1	s__Nodosilinea antarctica	76.227	195	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	98.34	98.34	0.86	0.86	2	-
GCF_015207395.1	s__Nodosilinea sp015207395	76.2177	181	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010671975.1	s__SIO4C1 sp010671975	76.1943	166	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__SIO4C1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696675.1	s__Nodosilinea tenue	76.189	160	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015207525.1	s__Nodosilinea sp015207525	76.1622	180	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032745.1	s__JAAUQQ01 sp012032745	75.7791	69	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-9006;f__Prochlorotrichaceae;g__JAAUQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314865.1	s__Phormidesmis priestleyi_B	75.6203	69	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534385.1	s__JACVSF01 sp014534385	75.6005	90	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACVSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935205.1	s__Cyanobium sp903935205	75.2781	50	1666	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.93	99.91	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-19 00:35:33,231] [INFO] GTDB search result was written to OceanDNA-b16201/result_gtdb.tsv
[2023-03-19 00:35:33,232] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:35:33,235] [INFO] DFAST_QC result json was written to OceanDNA-b16201/dqc_result.json
[2023-03-19 00:35:33,235] [INFO] DFAST_QC completed!
[2023-03-19 00:35:33,236] [INFO] Total running time: 0h2m14s