[2023-03-19 02:59:38,367] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,367] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference
[2023-03-19 02:59:39,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,461] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,461] [INFO] Running command: cat /var/lib/cwl/stg0703b945-6d8c-4d05-9e8f-4fd9ac6ce7f2/OceanDNA-b41003.fa | prodigal -d OceanDNA-b41003/cds.fna -a OceanDNA-b41003/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:00:05,133] [INFO] Task succeeded: Prodigal
[2023-03-19 03:00:05,133] [INFO] Task started: HMMsearch
[2023-03-19 03:00:05,133] [INFO] Running command: hmmsearch --tblout OceanDNA-b41003/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference/reference_markers.hmm OceanDNA-b41003/protein.faa > /dev/null
[2023-03-19 03:00:05,349] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:00:05,350] [INFO] Found 6/6 markers.
[2023-03-19 03:00:05,377] [INFO] Query marker FASTA was written to OceanDNA-b41003/markers.fasta
[2023-03-19 03:00:05,379] [INFO] Task started: Blastn
[2023-03-19 03:00:05,379] [INFO] Running command: blastn -query OceanDNA-b41003/markers.fasta -db /var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference/reference_markers.fasta -out OceanDNA-b41003/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:06,228] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:06,230] [INFO] Selected 15 target genomes.
[2023-03-19 03:00:06,230] [INFO] Target genome list was writen to OceanDNA-b41003/target_genomes.txt
[2023-03-19 03:00:06,239] [INFO] Task started: fastANI
[2023-03-19 03:00:06,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg0703b945-6d8c-4d05-9e8f-4fd9ac6ce7f2/OceanDNA-b41003.fa --refList OceanDNA-b41003/target_genomes.txt --output OceanDNA-b41003/fastani_result.tsv --threads 1
[2023-03-19 03:00:20,310] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:20,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:00:20,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:00:20,320] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:00:20,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:00:20,321] [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
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	92.9997	1222	1331	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	92.9959	1216	1331	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	89.0693	1138	1331	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	89.0332	1148	1331	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	88.8773	1118	1331	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	87.6981	1127	1331	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	87.6958	1124	1331	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	87.6266	1107	1331	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	87.522	1128	1331	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	87.4949	1143	1331	95	below_threshold
Pseudomonas extremaustralis	strain=14-3 substr. 14-3b	GCA_000242115.2	359110	359110	type	True	78.9285	497	1331	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_900102035.1	359110	359110	type	True	78.9221	502	1331	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	78.9094	501	1331	95	below_threshold
Pseudomonas extremaustralis		GCA_900625045.1	359110	359110	type	True	78.858	508	1331	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	75.859	97	1331	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:00:20,322] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41003/tc_result.tsv
[2023-03-19 03:00:20,323] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:00:20,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:00:20,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference/checkm_data
[2023-03-19 03:00:20,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:00:20,330] [INFO] Task started: CheckM
[2023-03-19 03:00:20,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41003/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41003/checkm_input OceanDNA-b41003/checkm_result
[2023-03-19 03:01:21,324] [INFO] Task succeeded: CheckM
[2023-03-19 03:01:21,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:01:21,330] [INFO] ===== Completeness check finished =====
[2023-03-19 03:01:21,330] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:01:21,330] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41003/markers.fasta)
[2023-03-19 03:01:21,331] [INFO] Task started: Blastn
[2023-03-19 03:01:21,331] [INFO] Running command: blastn -query OceanDNA-b41003/markers.fasta -db /var/lib/cwl/stg279242cb-04d1-4142-86fe-afcb66f66bb0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41003/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:01:22,758] [INFO] Task succeeded: Blastn
[2023-03-19 03:01:22,761] [INFO] Selected 19 target genomes.
[2023-03-19 03:01:22,761] [INFO] Target genome list was writen to OceanDNA-b41003/target_genomes_gtdb.txt
[2023-03-19 03:01:22,780] [INFO] Task started: fastANI
[2023-03-19 03:01:22,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg0703b945-6d8c-4d05-9e8f-4fd9ac6ce7f2/OceanDNA-b41003.fa --refList OceanDNA-b41003/target_genomes_gtdb.txt --output OceanDNA-b41003/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:01:41,119] [INFO] Task succeeded: fastANI
[2023-03-19 03:01:41,129] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:01:41,129] [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_000327065.1	s__Pseudomonas_A stutzeri_AE	98.1698	1277	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	conclusive
GCF_003696315.1	s__Pseudomonas_A songnenensis	92.9997	1222	1331	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	91.0054	1183	1331	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_013409135.1	s__Pseudomonas_A kunmingensis_A	89.2533	1174	1331	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_014764705.1	s__Pseudomonas_A sp002692525	89.0844	1129	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	89.0752	1138	1331	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_000935215.1	s__Pseudomonas_A stutzeri_AD	89.0741	1035	1331	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_007713455.1	s__Pseudomonas_A sp007713455	89.0649	1135	1331	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_002929225.1	s__Pseudomonas_A stutzeri_U	89.0342	1149	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0711	97.19	97.19	0.89	0.89	2	-
GCF_900114065.1	s__Pseudomonas_A kunmingensis	89.0189	1150	1331	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_002890795.1	s__Pseudomonas_A stutzeri_AA	88.6548	1168	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003488145.1	s__Pseudomonas_A sp003488145	88.2266	746	1331	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_015291885.1	s__Pseudomonas_A stutzeri_AC	87.7721	1120	1331	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_003205815.1	s__Pseudomonas_A sp003205815	87.5844	1156	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCA_002345575.1	s__Pseudomonas_A stutzeri_S	81.2695	738	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	79.7007	590	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102035.1	s__Pseudomonas_E extremaustralis	78.9051	504	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	98.99	0.98	0.92	5	-
GCF_003014615.1	s__Marinobacterium halophilum	75.8719	94	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:01:41,130] [INFO] GTDB search result was written to OceanDNA-b41003/result_gtdb.tsv
[2023-03-19 03:01:41,131] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:01:41,133] [INFO] DFAST_QC result json was written to OceanDNA-b41003/dqc_result.json
[2023-03-19 03:01:41,133] [INFO] DFAST_QC completed!
[2023-03-19 03:01:41,134] [INFO] Total running time: 0h2m3s