[2023-03-16 01:12:29,289] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,290] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference
[2023-03-16 01:12:30,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,462] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stg5aa737a5-a77c-4582-a0dc-dd006e55214b/OceanDNA-b40967.fa | prodigal -d OceanDNA-b40967/cds.fna -a OceanDNA-b40967/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:54,808] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:54,809] [INFO] Task started: HMMsearch
[2023-03-16 01:12:54,809] [INFO] Running command: hmmsearch --tblout OceanDNA-b40967/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference/reference_markers.hmm OceanDNA-b40967/protein.faa > /dev/null
[2023-03-16 01:12:55,021] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:55,022] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5aa737a5-a77c-4582-a0dc-dd006e55214b/OceanDNA-b40967.fa]
[2023-03-16 01:12:55,056] [INFO] Query marker FASTA was written to OceanDNA-b40967/markers.fasta
[2023-03-16 01:12:55,057] [INFO] Task started: Blastn
[2023-03-16 01:12:55,057] [INFO] Running command: blastn -query OceanDNA-b40967/markers.fasta -db /var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference/reference_markers.fasta -out OceanDNA-b40967/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:55,910] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:55,916] [INFO] Selected 9 target genomes.
[2023-03-16 01:12:55,917] [INFO] Target genome list was writen to OceanDNA-b40967/target_genomes.txt
[2023-03-16 01:12:55,931] [INFO] Task started: fastANI
[2023-03-16 01:12:55,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aa737a5-a77c-4582-a0dc-dd006e55214b/OceanDNA-b40967.fa --refList OceanDNA-b40967/target_genomes.txt --output OceanDNA-b40967/fastani_result.tsv --threads 1
[2023-03-16 01:13:04,703] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:04,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:13:04,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:13:04,710] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-03-16 01:13:04,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 01:13:04,710] [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
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	97.0577	1191	1325	95	conclusive
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	97.0405	1197	1325	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	96.9996	1203	1325	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	90.8119	1115	1325	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	90.7595	1114	1325	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	88.4435	1103	1325	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	88.4273	1108	1325	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	88.1497	1109	1325	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	88.1312	1097	1325	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:13:04,713] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40967/tc_result.tsv
[2023-03-16 01:13:04,716] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:13:04,717] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:13:04,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference/checkm_data
[2023-03-16 01:13:04,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:13:04,723] [INFO] Task started: CheckM
[2023-03-16 01:13:04,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40967/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40967/checkm_input OceanDNA-b40967/checkm_result
[2023-03-16 01:14:04,284] [INFO] Task succeeded: CheckM
[2023-03-16 01:14:04,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.28%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:14:04,288] [INFO] ===== Completeness check finished =====
[2023-03-16 01:14:04,288] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:14:04,288] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40967/markers.fasta)
[2023-03-16 01:14:04,290] [INFO] Task started: Blastn
[2023-03-16 01:14:04,290] [INFO] Running command: blastn -query OceanDNA-b40967/markers.fasta -db /var/lib/cwl/stg4b37c08d-990d-4fe6-a718-d0608ec89dc0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40967/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:14:05,981] [INFO] Task succeeded: Blastn
[2023-03-16 01:14:05,982] [INFO] Selected 16 target genomes.
[2023-03-16 01:14:05,982] [INFO] Target genome list was writen to OceanDNA-b40967/target_genomes_gtdb.txt
[2023-03-16 01:14:06,643] [INFO] Task started: fastANI
[2023-03-16 01:14:06,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aa737a5-a77c-4582-a0dc-dd006e55214b/OceanDNA-b40967.fa --refList OceanDNA-b40967/target_genomes_gtdb.txt --output OceanDNA-b40967/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:14:22,835] [INFO] Task succeeded: fastANI
[2023-03-16 01:14:22,844] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:14:22,844] [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_003205815.1	s__Pseudomonas_A sp003205815	97.2049	1210	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	conclusive
GCF_000219605.1	s__Pseudomonas_A stutzeri	90.8119	1115	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_000341615.1	s__Pseudomonas_A stutzeri_G	88.7941	1105	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	88.6765	1126	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	88.6187	1117	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	88.598	1126	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0711	97.19	97.19	0.89	0.89	2	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	88.5485	1123	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_900114065.1	s__Pseudomonas_A kunmingensis	88.431	1104	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.31	97.18	0.87	0.86	3	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	88.1497	1109	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	87.5069	1128	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.44	99.44	0.92	0.92	2	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	87.4413	1123	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	86.9056	1030	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_015291885.1	s__Pseudomonas_A stutzeri_AC	86.655	1081	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.94	97.56	0.91	0.88	14	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	86.5062	1030	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_002890795.1	s__Pseudomonas_A stutzeri_AA	85.8952	1076	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.6906	989	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-16 01:14:22,845] [INFO] GTDB search result was written to OceanDNA-b40967/result_gtdb.tsv
[2023-03-16 01:14:22,846] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:14:22,849] [INFO] DFAST_QC result json was written to OceanDNA-b40967/dqc_result.json
[2023-03-16 01:14:22,849] [INFO] DFAST_QC completed!
[2023-03-16 01:14:22,849] [INFO] Total running time: 0h1m54s