[2023-03-14 10:55:58,911] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference
[2023-03-14 10:56:00,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,754] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,754] [INFO] Running command: cat /var/lib/cwl/stge3553865-385a-48c9-a686-9fc5c1127fc2/OceanDNA-b40977.fa | prodigal -d OceanDNA-b40977/cds.fna -a OceanDNA-b40977/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:27,209] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:27,209] [INFO] Task started: HMMsearch
[2023-03-14 10:56:27,209] [INFO] Running command: hmmsearch --tblout OceanDNA-b40977/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference/reference_markers.hmm OceanDNA-b40977/protein.faa > /dev/null
[2023-03-14 10:56:27,584] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:27,584] [INFO] Found 6/6 markers.
[2023-03-14 10:56:27,640] [INFO] Query marker FASTA was written to OceanDNA-b40977/markers.fasta
[2023-03-14 10:56:27,640] [INFO] Task started: Blastn
[2023-03-14 10:56:27,640] [INFO] Running command: blastn -query OceanDNA-b40977/markers.fasta -db /var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference/reference_markers.fasta -out OceanDNA-b40977/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:28,644] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:28,645] [INFO] Selected 10 target genomes.
[2023-03-14 10:56:28,645] [INFO] Target genome list was writen to OceanDNA-b40977/target_genomes.txt
[2023-03-14 10:56:28,651] [INFO] Task started: fastANI
[2023-03-14 10:56:28,652] [INFO] Running command: fastANI --query /var/lib/cwl/stge3553865-385a-48c9-a686-9fc5c1127fc2/OceanDNA-b40977.fa --refList OceanDNA-b40977/target_genomes.txt --output OceanDNA-b40977/fastani_result.tsv --threads 1
[2023-03-14 10:56:38,342] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:38,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:38,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:38,349] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-03-14 10:56:38,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 10:56:38,349] [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 stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	97.3437	1228	1418	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	97.2926	1235	1418	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	91.4393	1124	1418	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	91.3995	1144	1418	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	91.3834	1144	1418	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	89.1757	1120	1418	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	89.0782	1120	1418	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.3619	895	1418	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	82.892	861	1418	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	81.2487	629	1418	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:38,350] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40977/tc_result.tsv
[2023-03-14 10:56:38,350] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:38,350] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:38,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference/checkm_data
[2023-03-14 10:56:38,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:38,363] [INFO] Task started: CheckM
[2023-03-14 10:56:38,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40977/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40977/checkm_input OceanDNA-b40977/checkm_result
[2023-03-14 10:57:43,315] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:43,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:43,536] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:43,536] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:43,537] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40977/markers.fasta)
[2023-03-14 10:57:43,537] [INFO] Task started: Blastn
[2023-03-14 10:57:43,537] [INFO] Running command: blastn -query OceanDNA-b40977/markers.fasta -db /var/lib/cwl/stgd9bebf60-979d-4ab0-b0c7-f67ad5fc1973/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40977/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:45,420] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:45,423] [INFO] Selected 14 target genomes.
[2023-03-14 10:57:45,423] [INFO] Target genome list was writen to OceanDNA-b40977/target_genomes_gtdb.txt
[2023-03-14 10:57:45,436] [INFO] Task started: fastANI
[2023-03-14 10:57:45,436] [INFO] Running command: fastANI --query /var/lib/cwl/stge3553865-385a-48c9-a686-9fc5c1127fc2/OceanDNA-b40977.fa --refList OceanDNA-b40977/target_genomes_gtdb.txt --output OceanDNA-b40977/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:59,758] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:59,767] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:59,767] [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_000219605.1	s__Pseudomonas_A stutzeri	97.3124	1234	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	conclusive
GCF_003205815.1	s__Pseudomonas_A sp003205815	90.8416	1126	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	89.1757	1120	1418	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_000935215.1	s__Pseudomonas_A stutzeri_AD	87.8139	1082	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	87.6704	1138	1418	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_002929225.1	s__Pseudomonas_A stutzeri_U	87.6645	1156	1418	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	87.6633	1149	1418	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_013409135.1	s__Pseudomonas_A kunmingensis_A	87.6504	1131	1418	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_000495915.1	s__Pseudomonas_A chloritidismutans	87.5944	1110	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	87.5183	1127	1418	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_002890915.1	s__Pseudomonas_A stutzeri_AF	87.23	1080	1418	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_000307775.2	s__Pseudomonas_A stutzeri_B	86.6071	1082	1418	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_015070855.1	s__Pseudomonas_A lopnurensis	86.0022	1033	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_002909485.1	s__Pseudomonas_A stutzeri_AH	85.7983	1126	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:59,768] [INFO] GTDB search result was written to OceanDNA-b40977/result_gtdb.tsv
[2023-03-14 10:57:59,768] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:59,769] [INFO] DFAST_QC result json was written to OceanDNA-b40977/dqc_result.json
[2023-03-14 10:57:59,769] [INFO] DFAST_QC completed!
[2023-03-14 10:57:59,769] [INFO] Total running time: 0h2m1s