[2023-03-15 08:59:47,030] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,030] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference
[2023-03-15 08:59:48,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,109] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,109] [INFO] Running command: cat /var/lib/cwl/stg7b199d93-9228-4a1e-9ad7-135860fd7c87/OceanDNA-b45813.fa | prodigal -d OceanDNA-b45813/cds.fna -a OceanDNA-b45813/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:08,775] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:08,775] [INFO] Task started: HMMsearch
[2023-03-15 09:00:08,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b45813/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference/reference_markers.hmm OceanDNA-b45813/protein.faa > /dev/null
[2023-03-15 09:00:08,947] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:08,948] [INFO] Found 6/6 markers.
[2023-03-15 09:00:08,964] [INFO] Query marker FASTA was written to OceanDNA-b45813/markers.fasta
[2023-03-15 09:00:08,964] [INFO] Task started: Blastn
[2023-03-15 09:00:08,964] [INFO] Running command: blastn -query OceanDNA-b45813/markers.fasta -db /var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference/reference_markers.fasta -out OceanDNA-b45813/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:09,559] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:09,560] [INFO] Selected 17 target genomes.
[2023-03-15 09:00:09,560] [INFO] Target genome list was writen to OceanDNA-b45813/target_genomes.txt
[2023-03-15 09:00:09,570] [INFO] Task started: fastANI
[2023-03-15 09:00:09,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b199d93-9228-4a1e-9ad7-135860fd7c87/OceanDNA-b45813.fa --refList OceanDNA-b45813/target_genomes.txt --output OceanDNA-b45813/fastani_result.tsv --threads 1
[2023-03-15 09:00:21,165] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:21,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:21,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:21,170] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:21,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:21,171] [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
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.3212	69	809	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.2156	68	809	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	76.1772	56	809	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.0436	80	809	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	75.9766	51	809	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:21,171] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45813/tc_result.tsv
[2023-03-15 09:00:21,171] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:21,171] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:21,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference/checkm_data
[2023-03-15 09:00:21,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:21,175] [INFO] Task started: CheckM
[2023-03-15 09:00:21,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45813/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45813/checkm_input OceanDNA-b45813/checkm_result
[2023-03-15 09:01:14,885] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:14,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:01:14,888] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:14,888] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:14,888] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45813/markers.fasta)
[2023-03-15 09:01:14,888] [INFO] Task started: Blastn
[2023-03-15 09:01:14,888] [INFO] Running command: blastn -query OceanDNA-b45813/markers.fasta -db /var/lib/cwl/stg727fd2cb-d32e-4cc8-8054-b00061012c39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45813/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:15,889] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:15,890] [INFO] Selected 23 target genomes.
[2023-03-15 09:01:15,891] [INFO] Target genome list was writen to OceanDNA-b45813/target_genomes_gtdb.txt
[2023-03-15 09:01:15,985] [INFO] Task started: fastANI
[2023-03-15 09:01:15,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b199d93-9228-4a1e-9ad7-135860fd7c87/OceanDNA-b45813.fa --refList OceanDNA-b45813/target_genomes_gtdb.txt --output OceanDNA-b45813/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:29,736] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:29,746] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:01:29,746] [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_002713695.1	s__Cephaloticoccus sp002713695	99.9869	805	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_002367815.1	s__Cephaloticoccus sp002367815	76.6998	119	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344205.1	s__UBA2377 sp002344205	76.3793	110	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903839035.1	s__Opi-474 sp903839035	76.2565	67	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.67	99.48	0.93	0.89	8	-
GCF_001580015.1	s__Cephaloticoccus primus	76.2156	68	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580045.1	s__Cephaloticoccus capnophilus	76.1772	56	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Cephaloticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859715.1	s__Opi-474 sp903859715	76.1586	79	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCA_003402695.1	s__Opi-474 sp003402695	76.1096	63	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902745.1	s__CAIUWA01 sp903902745	76.0967	63	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIUWA01	95.0	99.98	99.98	0.98	0.97	4	-
GCA_009695305.1	s__CAITWF01 sp009695305	76.0943	69	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559335.1	s__Rariglobus hedericola	76.0807	78	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862955.1	s__Opi-474 sp903862955	76.0348	72	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_903825285.1	s__Opi-474 sp903825285	75.9705	71	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_903855985.1	s__Opi-474 sp903855985	75.8603	68	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_016721945.1	s__Nibricoccus sp016721945	75.8223	51	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	75.7131	59	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003054665.1	s__EW11 sp003054665	75.703	53	809	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__EW11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:29,746] [INFO] GTDB search result was written to OceanDNA-b45813/result_gtdb.tsv
[2023-03-15 09:01:29,746] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:29,747] [INFO] DFAST_QC result json was written to OceanDNA-b45813/dqc_result.json
[2023-03-15 09:01:29,748] [INFO] DFAST_QC completed!
[2023-03-15 09:01:29,748] [INFO] Total running time: 0h1m43s