[2023-03-14 10:55:58,941] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,943] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference
[2023-03-14 10:56:00,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stge533ff8f-d2f1-4e39-8727-a9c9014ad01a/OceanDNA-b40959.fa | prodigal -d OceanDNA-b40959/cds.fna -a OceanDNA-b40959/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:26,957] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:26,957] [INFO] Task started: HMMsearch
[2023-03-14 10:56:26,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b40959/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference/reference_markers.hmm OceanDNA-b40959/protein.faa > /dev/null
[2023-03-14 10:56:27,266] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:27,267] [INFO] Found 6/6 markers.
[2023-03-14 10:56:27,293] [INFO] Query marker FASTA was written to OceanDNA-b40959/markers.fasta
[2023-03-14 10:56:27,293] [INFO] Task started: Blastn
[2023-03-14 10:56:27,293] [INFO] Running command: blastn -query OceanDNA-b40959/markers.fasta -db /var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference/reference_markers.fasta -out OceanDNA-b40959/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:28,221] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:28,222] [INFO] Selected 9 target genomes.
[2023-03-14 10:56:28,222] [INFO] Target genome list was writen to OceanDNA-b40959/target_genomes.txt
[2023-03-14 10:56:28,228] [INFO] Task started: fastANI
[2023-03-14 10:56:28,228] [INFO] Running command: fastANI --query /var/lib/cwl/stge533ff8f-d2f1-4e39-8727-a9c9014ad01a/OceanDNA-b40959.fa --refList OceanDNA-b40959/target_genomes.txt --output OceanDNA-b40959/fastani_result.tsv --threads 1
[2023-03-14 10:56:37,812] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:37,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:37,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:37,820] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-03-14 10:56:37,820] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-14 10:56:37,820] [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 kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	97.0198	1238	1399	95	inconclusive
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	96.9435	1254	1399	95	inconclusive
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	96.8097	1221	1399	95	inconclusive
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	89.078	1151	1399	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	89.0266	1174	1399	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	88.8446	1169	1399	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	88.6917	1198	1399	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	87.7175	1168	1399	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	87.6922	1170	1399	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:37,820] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40959/tc_result.tsv
[2023-03-14 10:56:37,820] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:37,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:37,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference/checkm_data
[2023-03-14 10:56:37,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:37,839] [INFO] Task started: CheckM
[2023-03-14 10:56:37,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40959/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40959/checkm_input OceanDNA-b40959/checkm_result
[2023-03-14 10:57:42,006] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:42,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:42,009] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:42,010] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:42,010] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40959/markers.fasta)
[2023-03-14 10:57:42,010] [INFO] Task started: Blastn
[2023-03-14 10:57:42,010] [INFO] Running command: blastn -query OceanDNA-b40959/markers.fasta -db /var/lib/cwl/stg613a8897-8a25-4bee-a4eb-ce463ac305ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40959/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:43,786] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:43,787] [INFO] Selected 10 target genomes.
[2023-03-14 10:57:43,787] [INFO] Target genome list was writen to OceanDNA-b40959/target_genomes_gtdb.txt
[2023-03-14 10:57:43,796] [INFO] Task started: fastANI
[2023-03-14 10:57:43,797] [INFO] Running command: fastANI --query /var/lib/cwl/stge533ff8f-d2f1-4e39-8727-a9c9014ad01a/OceanDNA-b40959.fa --refList OceanDNA-b40959/target_genomes_gtdb.txt --output OceanDNA-b40959/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:54,117] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:54,123] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-14 10:57:54,124] [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_014764705.1	s__Pseudomonas_A sp002692525	98.3188	1281	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	inconclusive
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	97.1314	1271	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	inconclusive
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	97.0625	1254	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	inconclusive
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	97.001	1261	1399	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	96.9795	1249	1399	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	96.9435	1254	1399	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_000495915.1	s__Pseudomonas_A chloritidismutans	96.8043	1221	1399	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_000935215.1	s__Pseudomonas_A stutzeri_AD	96.7993	1147	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCA_003488145.1	s__Pseudomonas_A sp003488145	96.2804	784	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.7169	97.61	97.61	0.74	0.74	2	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	87.7167	1169	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:54,124] [INFO] GTDB search result was written to OceanDNA-b40959/result_gtdb.tsv
[2023-03-14 10:57:54,124] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:54,125] [INFO] DFAST_QC result json was written to OceanDNA-b40959/dqc_result.json
[2023-03-14 10:57:54,125] [INFO] DFAST_QC completed!
[2023-03-14 10:57:54,125] [INFO] Total running time: 0h1m55s