[2023-03-18 01:41:20,937] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,937] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference
[2023-03-18 01:41:22,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,075] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,075] [INFO] Running command: cat /var/lib/cwl/stg0038c8e8-a84b-4b25-8f6e-792b6258ab83/OceanDNA-b41152.fa | prodigal -d OceanDNA-b41152/cds.fna -a OceanDNA-b41152/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:45,172] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:45,172] [INFO] Task started: HMMsearch
[2023-03-18 01:41:45,172] [INFO] Running command: hmmsearch --tblout OceanDNA-b41152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference/reference_markers.hmm OceanDNA-b41152/protein.faa > /dev/null
[2023-03-18 01:41:45,385] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:45,386] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0038c8e8-a84b-4b25-8f6e-792b6258ab83/OceanDNA-b41152.fa]
[2023-03-18 01:41:45,407] [INFO] Query marker FASTA was written to OceanDNA-b41152/markers.fasta
[2023-03-18 01:41:45,408] [INFO] Task started: Blastn
[2023-03-18 01:41:45,408] [INFO] Running command: blastn -query OceanDNA-b41152/markers.fasta -db /var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference/reference_markers.fasta -out OceanDNA-b41152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:46,165] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:46,166] [INFO] Selected 12 target genomes.
[2023-03-18 01:41:46,166] [INFO] Target genome list was writen to OceanDNA-b41152/target_genomes.txt
[2023-03-18 01:41:46,175] [INFO] Task started: fastANI
[2023-03-18 01:41:46,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg0038c8e8-a84b-4b25-8f6e-792b6258ab83/OceanDNA-b41152.fa --refList OceanDNA-b41152/target_genomes.txt --output OceanDNA-b41152/fastani_result.tsv --threads 1
[2023-03-18 01:41:56,454] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:56,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:56,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:56,462] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 01:41:56,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:41:56,462] [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
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	96.0105	1077	1233	95	conclusive
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	95.9719	1046	1233	95	conclusive
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	83.8576	840	1233	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	83.826	844	1233	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	83.5802	871	1233	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	83.4908	883	1233	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.8492	384	1233	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	78.6608	428	1233	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.6439	435	1233	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	78.4213	342	1233	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	78.4044	346	1233	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.3733	385	1233	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:56,462] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41152/tc_result.tsv
[2023-03-18 01:41:56,463] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:56,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:56,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference/checkm_data
[2023-03-18 01:41:56,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:56,469] [INFO] Task started: CheckM
[2023-03-18 01:41:56,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41152/checkm_input OceanDNA-b41152/checkm_result
[2023-03-18 01:42:54,646] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:54,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:54,649] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:54,649] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:54,649] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41152/markers.fasta)
[2023-03-18 01:42:54,650] [INFO] Task started: Blastn
[2023-03-18 01:42:54,650] [INFO] Running command: blastn -query OceanDNA-b41152/markers.fasta -db /var/lib/cwl/stg944c061b-c290-47e2-a8be-1d5f6d096e9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:55,906] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:55,907] [INFO] Selected 7 target genomes.
[2023-03-18 01:42:55,907] [INFO] Target genome list was writen to OceanDNA-b41152/target_genomes_gtdb.txt
[2023-03-18 01:42:55,913] [INFO] Task started: fastANI
[2023-03-18 01:42:55,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg0038c8e8-a84b-4b25-8f6e-792b6258ab83/OceanDNA-b41152.fa --refList OceanDNA-b41152/target_genomes_gtdb.txt --output OceanDNA-b41152/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:43:02,421] [INFO] Task succeeded: fastANI
[2023-03-18 01:43:02,426] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:43:02,426] [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_900114765.1	s__Pseudomonas_D pachastrellae	96.0302	1076	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	conclusive
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	90.1751	1098	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	87.9868	840	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	83.8073	846	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_002903165.1	s__Pseudomonas_D oceani	83.5941	869	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	81.1808	715	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592875.1	s__Pseudomonas_E sp001592875	78.6168	402	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:43:02,426] [INFO] GTDB search result was written to OceanDNA-b41152/result_gtdb.tsv
[2023-03-18 01:43:02,426] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:43:02,427] [INFO] DFAST_QC result json was written to OceanDNA-b41152/dqc_result.json
[2023-03-18 01:43:02,427] [INFO] DFAST_QC completed!
[2023-03-18 01:43:02,427] [INFO] Total running time: 0h1m41s