[2023-03-14 13:08:46,505] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:08:46,505] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:08:46,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference
[2023-03-14 13:08:47,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:08:47,601] [INFO] Task started: Prodigal
[2023-03-14 13:08:47,601] [INFO] Running command: cat /var/lib/cwl/stg33f6583d-a0d6-4a0c-b60b-e10e0be189a9/OceanDNA-b8880.fa | prodigal -d OceanDNA-b8880/cds.fna -a OceanDNA-b8880/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:08:52,481] [INFO] Task succeeded: Prodigal
[2023-03-14 13:08:52,482] [INFO] Task started: HMMsearch
[2023-03-14 13:08:52,482] [INFO] Running command: hmmsearch --tblout OceanDNA-b8880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference/reference_markers.hmm OceanDNA-b8880/protein.faa > /dev/null
[2023-03-14 13:08:52,637] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:08:52,638] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg33f6583d-a0d6-4a0c-b60b-e10e0be189a9/OceanDNA-b8880.fa]
[2023-03-14 13:08:52,646] [INFO] Query marker FASTA was written to OceanDNA-b8880/markers.fasta
[2023-03-14 13:08:52,648] [INFO] Task started: Blastn
[2023-03-14 13:08:52,648] [INFO] Running command: blastn -query OceanDNA-b8880/markers.fasta -db /var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference/reference_markers.fasta -out OceanDNA-b8880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:08:53,208] [INFO] Task succeeded: Blastn
[2023-03-14 13:08:53,210] [INFO] Selected 21 target genomes.
[2023-03-14 13:08:53,210] [INFO] Target genome list was writen to OceanDNA-b8880/target_genomes.txt
[2023-03-14 13:08:53,247] [INFO] Task started: fastANI
[2023-03-14 13:08:53,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg33f6583d-a0d6-4a0c-b60b-e10e0be189a9/OceanDNA-b8880.fa --refList OceanDNA-b8880/target_genomes.txt --output OceanDNA-b8880/fastani_result.tsv --threads 1
[2023-03-14 13:09:04,457] [INFO] Task succeeded: fastANI
[2023-03-14 13:09:04,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:09:04,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:09:04,458] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:09:04,458] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:09:04,458] [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
--------------------------------------------------------------------------------
[2023-03-14 13:09:04,459] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8880/tc_result.tsv
[2023-03-14 13:09:04,459] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:09:04,459] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:09:04,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference/checkm_data
[2023-03-14 13:09:04,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:09:04,512] [INFO] Task started: CheckM
[2023-03-14 13:09:04,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8880/checkm_input OceanDNA-b8880/checkm_result
[2023-03-14 13:09:28,841] [INFO] Task succeeded: CheckM
[2023-03-14 13:09:28,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:09:28,845] [INFO] ===== Completeness check finished =====
[2023-03-14 13:09:28,846] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:09:28,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8880/markers.fasta)
[2023-03-14 13:09:28,847] [INFO] Task started: Blastn
[2023-03-14 13:09:28,847] [INFO] Running command: blastn -query OceanDNA-b8880/markers.fasta -db /var/lib/cwl/stg258d4cec-8f02-4f33-bba7-67c88b33e3e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:09:31,222] [INFO] Task succeeded: Blastn
[2023-03-14 13:09:31,223] [INFO] Selected 16 target genomes.
[2023-03-14 13:09:31,223] [INFO] Target genome list was writen to OceanDNA-b8880/target_genomes_gtdb.txt
[2023-03-14 13:09:31,240] [INFO] Task started: fastANI
[2023-03-14 13:09:31,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg33f6583d-a0d6-4a0c-b60b-e10e0be189a9/OceanDNA-b8880.fa --refList OceanDNA-b8880/target_genomes_gtdb.txt --output OceanDNA-b8880/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:09:39,393] [INFO] Task succeeded: fastANI
[2023-03-14 13:09:39,400] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:09:39,400] [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_902622575.1	s__MED-G14 sp902622575	95.9731	202	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902574335.1	s__MED-G14 sp902574335	81.8985	111	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595555.1	s__MED-G14 sp902595555	81.5517	185	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.27	95.29	0.86	0.83	8	-
GCA_902597545.1	s__MED-G14 sp902597545	78.317	137	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
GCA_902546095.1	s__MED-G14 sp902546095	78.3144	104	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	78.241	101	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902610105.1	s__MED-G14 sp902610105	78.2158	64	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535165.1	s__MED-G14 sp902535165	78.091	121	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606555.1	s__MED-G14 sp902606555	78.0828	85	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587325.1	s__MED-G14 sp902587325	76.5261	63	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.53	95.17	0.82	0.78	10	-
--------------------------------------------------------------------------------
[2023-03-14 13:09:39,402] [INFO] GTDB search result was written to OceanDNA-b8880/result_gtdb.tsv
[2023-03-14 13:09:39,402] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:09:39,404] [INFO] DFAST_QC result json was written to OceanDNA-b8880/dqc_result.json
[2023-03-14 13:09:39,404] [INFO] DFAST_QC completed!
[2023-03-14 13:09:39,404] [INFO] Total running time: 0h0m53s