[2023-03-18 03:28:30,804] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference
[2023-03-18 03:28:31,900] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,900] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,900] [INFO] Running command: cat /var/lib/cwl/stg0b95823d-4aa6-4780-a673-c9c30d693280/OceanDNA-b16158.fa | prodigal -d OceanDNA-b16158/cds.fna -a OceanDNA-b16158/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:56,641] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:56,641] [INFO] Task started: HMMsearch
[2023-03-18 03:28:56,641] [INFO] Running command: hmmsearch --tblout OceanDNA-b16158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference/reference_markers.hmm OceanDNA-b16158/protein.faa > /dev/null
[2023-03-18 03:28:56,877] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:56,877] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b95823d-4aa6-4780-a673-c9c30d693280/OceanDNA-b16158.fa]
[2023-03-18 03:28:56,905] [INFO] Query marker FASTA was written to OceanDNA-b16158/markers.fasta
[2023-03-18 03:28:56,905] [INFO] Task started: Blastn
[2023-03-18 03:28:56,905] [INFO] Running command: blastn -query OceanDNA-b16158/markers.fasta -db /var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference/reference_markers.fasta -out OceanDNA-b16158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:57,415] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:57,416] [INFO] Selected 22 target genomes.
[2023-03-18 03:28:57,416] [INFO] Target genome list was writen to OceanDNA-b16158/target_genomes.txt
[2023-03-18 03:28:57,427] [INFO] Task started: fastANI
[2023-03-18 03:28:57,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b95823d-4aa6-4780-a673-c9c30d693280/OceanDNA-b16158.fa --refList OceanDNA-b16158/target_genomes.txt --output OceanDNA-b16158/fastani_result.tsv --threads 1
[2023-03-18 03:29:13,869] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:13,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:29:13,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:29:13,873] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:29:13,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:29:13,873] [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
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.9798	145	1208	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.6229	67	1208	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:29:13,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16158/tc_result.tsv
[2023-03-18 03:29:13,873] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:29:13,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:29:13,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference/checkm_data
[2023-03-18 03:29:13,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:29:13,880] [INFO] Task started: CheckM
[2023-03-18 03:29:13,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16158/checkm_input OceanDNA-b16158/checkm_result
[2023-03-18 03:30:16,554] [INFO] Task succeeded: CheckM
[2023-03-18 03:30:16,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:30:16,557] [INFO] ===== Completeness check finished =====
[2023-03-18 03:30:16,557] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:30:16,557] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16158/markers.fasta)
[2023-03-18 03:30:16,557] [INFO] Task started: Blastn
[2023-03-18 03:30:16,557] [INFO] Running command: blastn -query OceanDNA-b16158/markers.fasta -db /var/lib/cwl/stg070b54a7-a071-44d9-a4a3-4bf48af02de6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:30:17,252] [INFO] Task succeeded: Blastn
[2023-03-18 03:30:17,253] [INFO] Selected 31 target genomes.
[2023-03-18 03:30:17,253] [INFO] Target genome list was writen to OceanDNA-b16158/target_genomes_gtdb.txt
[2023-03-18 03:30:17,370] [INFO] Task started: fastANI
[2023-03-18 03:30:17,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b95823d-4aa6-4780-a673-c9c30d693280/OceanDNA-b16158.fa --refList OceanDNA-b16158/target_genomes_gtdb.txt --output OceanDNA-b16158/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:30:43,083] [INFO] Task succeeded: fastANI
[2023-03-18 03:30:43,091] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:30:43,091] [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_000332055.1	s__Xenococcus sp000332055	81.1178	786	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Xenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659865.1	s__Hyella patelloides	76.471	214	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002110465.1	s__Rippkaea sp002110465	76.4063	51	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	76.2604	201	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	75.9752	144	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.9707	140	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368355.1	s__Pleurocapsa sp002368355	75.8172	91	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169335.1	s__Crocosphaera chwakensis	75.6193	65	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003995.1	s__Pleurocapsa sp003003995	75.5769	97	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672865.1	s__SIO1D9 sp010672865	75.5711	58	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	75.3518	91	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCA_010672525.1	s__Okeania sp010672525	75.1645	69	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864295.1	s__Aphanothece_B sacrum	75.1205	52	1208	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Aphanothece_B	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:30:43,091] [INFO] GTDB search result was written to OceanDNA-b16158/result_gtdb.tsv
[2023-03-18 03:30:43,091] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:30:43,092] [INFO] DFAST_QC result json was written to OceanDNA-b16158/dqc_result.json
[2023-03-18 03:30:43,092] [INFO] DFAST_QC completed!
[2023-03-18 03:30:43,092] [INFO] Total running time: 0h2m12s