[2023-03-18 23:50:29,205] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:50:29,208] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:50:29,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference
[2023-03-18 23:50:30,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:50:30,481] [INFO] Task started: Prodigal
[2023-03-18 23:50:30,481] [INFO] Running command: cat /var/lib/cwl/stga8a24509-8b23-4ce0-b6d6-ef8715a2cc37/OceanDNA-b5248.fa | prodigal -d OceanDNA-b5248/cds.fna -a OceanDNA-b5248/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:50:54,612] [INFO] Task succeeded: Prodigal
[2023-03-18 23:50:54,612] [INFO] Task started: HMMsearch
[2023-03-18 23:50:54,612] [INFO] Running command: hmmsearch --tblout OceanDNA-b5248/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference/reference_markers.hmm OceanDNA-b5248/protein.faa > /dev/null
[2023-03-18 23:50:54,820] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:50:54,820] [INFO] Found 6/6 markers.
[2023-03-18 23:50:54,850] [INFO] Query marker FASTA was written to OceanDNA-b5248/markers.fasta
[2023-03-18 23:50:54,851] [INFO] Task started: Blastn
[2023-03-18 23:50:54,851] [INFO] Running command: blastn -query OceanDNA-b5248/markers.fasta -db /var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference/reference_markers.fasta -out OceanDNA-b5248/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:50:55,401] [INFO] Task succeeded: Blastn
[2023-03-18 23:50:55,402] [INFO] Selected 29 target genomes.
[2023-03-18 23:50:55,403] [INFO] Target genome list was writen to OceanDNA-b5248/target_genomes.txt
[2023-03-18 23:50:55,422] [INFO] Task started: fastANI
[2023-03-18 23:50:55,422] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a24509-8b23-4ce0-b6d6-ef8715a2cc37/OceanDNA-b5248.fa --refList OceanDNA-b5248/target_genomes.txt --output OceanDNA-b5248/fastani_result.tsv --threads 1
[2023-03-18 23:51:11,648] [INFO] Task succeeded: fastANI
[2023-03-18 23:51:11,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:51:11,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:51:11,653] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:51:11,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:51:11,653] [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
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	75.9089	69	1174	95	below_threshold
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	75.8128	101	1174	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:51:11,653] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5248/tc_result.tsv
[2023-03-18 23:51:11,653] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:51:11,653] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:51:11,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference/checkm_data
[2023-03-18 23:51:11,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:51:11,659] [INFO] Task started: CheckM
[2023-03-18 23:51:11,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5248/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5248/checkm_input OceanDNA-b5248/checkm_result
[2023-03-18 23:52:12,224] [INFO] Task succeeded: CheckM
[2023-03-18 23:52:12,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:52:12,244] [INFO] ===== Completeness check finished =====
[2023-03-18 23:52:12,244] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:52:12,244] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5248/markers.fasta)
[2023-03-18 23:52:12,245] [INFO] Task started: Blastn
[2023-03-18 23:52:12,245] [INFO] Running command: blastn -query OceanDNA-b5248/markers.fasta -db /var/lib/cwl/stg13e5f1d7-642c-4270-8484-fb99b1ca0a2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5248/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:52:13,006] [INFO] Task succeeded: Blastn
[2023-03-18 23:52:13,007] [INFO] Selected 28 target genomes.
[2023-03-18 23:52:13,007] [INFO] Target genome list was writen to OceanDNA-b5248/target_genomes_gtdb.txt
[2023-03-18 23:52:13,053] [INFO] Task started: fastANI
[2023-03-18 23:52:13,053] [INFO] Running command: fastANI --query /var/lib/cwl/stga8a24509-8b23-4ce0-b6d6-ef8715a2cc37/OceanDNA-b5248.fa --refList OceanDNA-b5248/target_genomes_gtdb.txt --output OceanDNA-b5248/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:52:27,204] [INFO] Task succeeded: fastANI
[2023-03-18 23:52:27,210] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:52:27,210] [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
GCA_016709005.1	s__JADJGJ01 sp016709005	76.803	221	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	98.05	97.64	0.91	0.88	3	-
GCA_016719925.1	s__JADJGJ01 sp016719925	76.604	155	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192075.1	s__JADJGJ01 sp016192075	76.2357	159	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708105.1	s__JADJGJ01 sp016708105	76.1841	155	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	99.76	99.76	0.97	0.97	2	-
GCA_905478225.1	s__Crocinitomix sp905478225	76.0084	88	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	75.9263	68	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138735.1	s__Crocinitomix sp013138735	75.9037	90	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621625.1	s__Crocinitomix catalasitica	75.8128	101	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662905.1	s__Putridiphycobacter sp015662905	75.5665	54	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:52:27,211] [INFO] GTDB search result was written to OceanDNA-b5248/result_gtdb.tsv
[2023-03-18 23:52:27,211] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:52:27,213] [INFO] DFAST_QC result json was written to OceanDNA-b5248/dqc_result.json
[2023-03-18 23:52:27,213] [INFO] DFAST_QC completed!
[2023-03-18 23:52:27,213] [INFO] Total running time: 0h1m58s