[2023-03-15 17:24:01,408] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,409] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,409] [INFO] DQC Reference Directory: /var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference
[2023-03-15 17:24:02,604] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,605] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,605] [INFO] Running command: cat /var/lib/cwl/stg080ca52b-efac-41cb-86f4-66ff053bff17/OceanDNA-b16165.fa | prodigal -d OceanDNA-b16165/cds.fna -a OceanDNA-b16165/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:27,805] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:27,805] [INFO] Task started: HMMsearch
[2023-03-15 17:24:27,806] [INFO] Running command: hmmsearch --tblout OceanDNA-b16165/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference/reference_markers.hmm OceanDNA-b16165/protein.faa > /dev/null
[2023-03-15 17:24:28,139] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:28,140] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg080ca52b-efac-41cb-86f4-66ff053bff17/OceanDNA-b16165.fa]
[2023-03-15 17:24:28,169] [INFO] Query marker FASTA was written to OceanDNA-b16165/markers.fasta
[2023-03-15 17:24:28,170] [INFO] Task started: Blastn
[2023-03-15 17:24:28,170] [INFO] Running command: blastn -query OceanDNA-b16165/markers.fasta -db /var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference/reference_markers.fasta -out OceanDNA-b16165/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:28,818] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:28,818] [INFO] Selected 23 target genomes.
[2023-03-15 17:24:28,819] [INFO] Target genome list was writen to OceanDNA-b16165/target_genomes.txt
[2023-03-15 17:24:28,833] [INFO] Task started: fastANI
[2023-03-15 17:24:28,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg080ca52b-efac-41cb-86f4-66ff053bff17/OceanDNA-b16165.fa --refList OceanDNA-b16165/target_genomes.txt --output OceanDNA-b16165/fastani_result.tsv --threads 1
[2023-03-15 17:24:44,931] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:44,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:44,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:44,938] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:44,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:24:44,938] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	75.9522	205	1630	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.4893	75	1630	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.4314	73	1630	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.3601	72	1630	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.3418	60	1630	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.3418	60	1630	95	below_threshold
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	75.2658	57	1630	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	75.0953	50	1630	95	below_threshold
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	75.017	81	1630	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:44,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16165/tc_result.tsv
[2023-03-15 17:24:44,938] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:44,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:44,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference/checkm_data
[2023-03-15 17:24:44,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:44,945] [INFO] Task started: CheckM
[2023-03-15 17:24:44,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16165/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16165/checkm_input OceanDNA-b16165/checkm_result
[2023-03-15 17:25:45,434] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:45,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:45,438] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:45,438] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:45,438] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16165/markers.fasta)
[2023-03-15 17:25:45,438] [INFO] Task started: Blastn
[2023-03-15 17:25:45,438] [INFO] Running command: blastn -query OceanDNA-b16165/markers.fasta -db /var/lib/cwl/stgb177669d-4d26-4832-877b-c270b1949dfe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16165/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:46,160] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:46,161] [INFO] Selected 17 target genomes.
[2023-03-15 17:25:46,161] [INFO] Target genome list was writen to OceanDNA-b16165/target_genomes_gtdb.txt
[2023-03-15 17:25:46,175] [INFO] Task started: fastANI
[2023-03-15 17:25:46,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg080ca52b-efac-41cb-86f4-66ff053bff17/OceanDNA-b16165.fa --refList OceanDNA-b16165/target_genomes_gtdb.txt --output OceanDNA-b16165/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:26:03,022] [INFO] Task succeeded: fastANI
[2023-03-15 17:26:03,030] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:26:03,030] [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_900659865.1	s__Hyella patelloides	78.6183	752	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	77.9733	543	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207195.1	s__Pleurocapsa sp015207195	76.1307	209	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332055.1	s__Xenococcus sp000332055	76.0011	168	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Xenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368355.1	s__Pleurocapsa sp002368355	75.9029	154	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.6255	133	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__LEGE-06147	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031035.1	s__Hydrococcus sp012031035	75.3635	79	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Hydrococcus	95.0	99.84	99.83	0.93	0.93	3	-
GCF_000021825.1	s__Gloeothece citriformis	75.3511	73	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Gloeothece	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672865.1	s__SIO1D9 sp010672865	75.3472	77	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147335.1	s__Gloeothece verrucosa	75.2658	57	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Gloeothece	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007785.1	s__Chroococcus hegewaldii	75.2412	70	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Chroococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014132355.1	s__Okeania sp014132355	75.1745	77	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207665.1	s__Rivularia radiosum	75.1115	73	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003838195.1	s__Okeania hirsuta	75.017	81	1630	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	98.05	95.33	0.88	0.84	10	-
--------------------------------------------------------------------------------
[2023-03-15 17:26:03,031] [INFO] GTDB search result was written to OceanDNA-b16165/result_gtdb.tsv
[2023-03-15 17:26:03,031] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:26:03,032] [INFO] DFAST_QC result json was written to OceanDNA-b16165/dqc_result.json
[2023-03-15 17:26:03,032] [INFO] DFAST_QC completed!
[2023-03-15 17:26:03,032] [INFO] Total running time: 0h2m2s