[2023-03-18 02:48:47,727] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:47,727] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:47,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference
[2023-03-18 02:48:49,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:49,546] [INFO] Task started: Prodigal
[2023-03-18 02:48:49,546] [INFO] Running command: cat /var/lib/cwl/stg8d63ac3c-705f-4fe8-9af8-82c436153c2e/OceanDNA-b13087.fa | prodigal -d OceanDNA-b13087/cds.fna -a OceanDNA-b13087/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:49:03,878] [INFO] Task succeeded: Prodigal
[2023-03-18 02:49:03,878] [INFO] Task started: HMMsearch
[2023-03-18 02:49:03,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b13087/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference/reference_markers.hmm OceanDNA-b13087/protein.faa > /dev/null
[2023-03-18 02:49:04,033] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:49:04,033] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8d63ac3c-705f-4fe8-9af8-82c436153c2e/OceanDNA-b13087.fa]
[2023-03-18 02:49:04,058] [INFO] Query marker FASTA was written to OceanDNA-b13087/markers.fasta
[2023-03-18 02:49:04,058] [INFO] Task started: Blastn
[2023-03-18 02:49:04,058] [INFO] Running command: blastn -query OceanDNA-b13087/markers.fasta -db /var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference/reference_markers.fasta -out OceanDNA-b13087/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:04,634] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:04,635] [INFO] Selected 17 target genomes.
[2023-03-18 02:49:04,635] [INFO] Target genome list was writen to OceanDNA-b13087/target_genomes.txt
[2023-03-18 02:49:04,645] [INFO] Task started: fastANI
[2023-03-18 02:49:04,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d63ac3c-705f-4fe8-9af8-82c436153c2e/OceanDNA-b13087.fa --refList OceanDNA-b13087/target_genomes.txt --output OceanDNA-b13087/fastani_result.tsv --threads 1
[2023-03-18 02:49:19,098] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:19,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:19,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:19,108] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:19,108] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:49:19,109] [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
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	78.723	310	598	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	78.2215	366	598	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.9719	113	598	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.897	240	598	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	74.8091	130	598	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.8054	172	598	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	74.8032	94	598	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	74.7876	82	598	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	74.7624	122	598	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	74.7377	61	598	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	74.7163	57	598	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	74.6847	104	598	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	74.678	136	598	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	74.6644	133	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:49:19,109] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13087/tc_result.tsv
[2023-03-18 02:49:19,131] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:19,131] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:19,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference/checkm_data
[2023-03-18 02:49:19,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:19,148] [INFO] Task started: CheckM
[2023-03-18 02:49:19,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13087/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13087/checkm_input OceanDNA-b13087/checkm_result
[2023-03-18 02:49:56,313] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:56,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:56,315] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:56,316] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:56,316] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13087/markers.fasta)
[2023-03-18 02:49:56,317] [INFO] Task started: Blastn
[2023-03-18 02:49:56,317] [INFO] Running command: blastn -query OceanDNA-b13087/markers.fasta -db /var/lib/cwl/stg9ae8286d-420f-451e-aaed-ca25f48c16c5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13087/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:57,141] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:57,141] [INFO] Selected 10 target genomes.
[2023-03-18 02:49:57,141] [INFO] Target genome list was writen to OceanDNA-b13087/target_genomes_gtdb.txt
[2023-03-18 02:49:57,258] [INFO] Task started: fastANI
[2023-03-18 02:49:57,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d63ac3c-705f-4fe8-9af8-82c436153c2e/OceanDNA-b13087.fa --refList OceanDNA-b13087/target_genomes_gtdb.txt --output OceanDNA-b13087/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:50:04,014] [INFO] Task succeeded: fastANI
[2023-03-18 02:50:04,019] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:50:04,020] [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_002257665.1	s__Rubricoccus marinus	78.7097	311	598	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960515.1	s__Rubricoccus sp012960515	78.6548	309	598	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	78.3289	330	598	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCF_002283365.1	s__Rubrivirga marina	78.2165	367	598	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	77.8335	281	598	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	74.8269	149	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	74.8099	83	598	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2023-03-18 02:50:04,020] [INFO] GTDB search result was written to OceanDNA-b13087/result_gtdb.tsv
[2023-03-18 02:50:04,020] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:50:04,021] [INFO] DFAST_QC result json was written to OceanDNA-b13087/dqc_result.json
[2023-03-18 02:50:04,021] [INFO] DFAST_QC completed!
[2023-03-18 02:50:04,021] [INFO] Total running time: 0h1m16s