[2023-03-16 04:20:43,520] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,520] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference
[2023-03-16 04:20:44,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,609] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,609] [INFO] Running command: cat /var/lib/cwl/stgd5ccd750-d09f-4677-bc9c-df976ccfde94/OceanDNA-b17991.fa | prodigal -d OceanDNA-b17991/cds.fna -a OceanDNA-b17991/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:20:49,045] [INFO] Task succeeded: Prodigal
[2023-03-16 04:20:49,046] [INFO] Task started: HMMsearch
[2023-03-16 04:20:49,046] [INFO] Running command: hmmsearch --tblout OceanDNA-b17991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference/reference_markers.hmm OceanDNA-b17991/protein.faa > /dev/null
[2023-03-16 04:20:49,197] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:20:49,198] [INFO] Found 6/6 markers.
[2023-03-16 04:20:49,205] [INFO] Query marker FASTA was written to OceanDNA-b17991/markers.fasta
[2023-03-16 04:20:49,205] [INFO] Task started: Blastn
[2023-03-16 04:20:49,205] [INFO] Running command: blastn -query OceanDNA-b17991/markers.fasta -db /var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference/reference_markers.fasta -out OceanDNA-b17991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:20:49,724] [INFO] Task succeeded: Blastn
[2023-03-16 04:20:49,724] [INFO] Selected 19 target genomes.
[2023-03-16 04:20:49,725] [INFO] Target genome list was writen to OceanDNA-b17991/target_genomes.txt
[2023-03-16 04:20:49,734] [INFO] Task started: fastANI
[2023-03-16 04:20:49,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ccd750-d09f-4677-bc9c-df976ccfde94/OceanDNA-b17991.fa --refList OceanDNA-b17991/target_genomes.txt --output OceanDNA-b17991/fastani_result.tsv --threads 1
[2023-03-16 04:20:56,601] [INFO] Task succeeded: fastANI
[2023-03-16 04:20:56,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:20:56,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:20:56,602] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:20:56,602] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:20:56,602] [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
--------------------------------------------------------------------------------
[2023-03-16 04:20:56,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17991/tc_result.tsv
[2023-03-16 04:20:56,602] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:20:56,602] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:20:56,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference/checkm_data
[2023-03-16 04:20:56,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:20:56,608] [INFO] Task started: CheckM
[2023-03-16 04:20:56,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17991/checkm_input OceanDNA-b17991/checkm_result
[2023-03-16 04:21:13,563] [INFO] Task succeeded: CheckM
[2023-03-16 04:21:13,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:21:13,564] [INFO] ===== Completeness check finished =====
[2023-03-16 04:21:13,565] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:21:13,565] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17991/markers.fasta)
[2023-03-16 04:21:13,565] [INFO] Task started: Blastn
[2023-03-16 04:21:13,565] [INFO] Running command: blastn -query OceanDNA-b17991/markers.fasta -db /var/lib/cwl/stg989927cd-2dd4-49c4-a4e9-7d7d08ce40a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:14,303] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:14,304] [INFO] Selected 19 target genomes.
[2023-03-16 04:21:14,304] [INFO] Target genome list was writen to OceanDNA-b17991/target_genomes_gtdb.txt
[2023-03-16 04:21:14,329] [INFO] Task started: fastANI
[2023-03-16 04:21:14,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ccd750-d09f-4677-bc9c-df976ccfde94/OceanDNA-b17991.fa --refList OceanDNA-b17991/target_genomes_gtdb.txt --output OceanDNA-b17991/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:21:18,751] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:18,758] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:21:18,758] [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_012963075.1	s__Marinisoma sp012963075	97.5593	155	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002348725.1	s__Marinisoma sp002348725	79.9829	153	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.66	99.62	0.84	0.83	4	-
GCA_902575395.1	s__Marinisoma sp902575395	79.7447	153	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701645.1	s__Marinisoma sp002701645	78.5318	99	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182795.1	s__Marinisoma sp905182795	78.0871	114	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402755.1	s__Marinisoma sp000402755	77.8332	104	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_000402815.1	s__Marinisoma atlanticum	77.4371	100	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_902576865.1	s__Marinisoma sp902576865	76.9043	60	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902538565.1	s__Marinisoma sp902538565	76.6847	70	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_902624275.1	s__Marinisoma sp902624275	76.6083	69	283	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:21:18,758] [INFO] GTDB search result was written to OceanDNA-b17991/result_gtdb.tsv
[2023-03-16 04:21:18,758] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:21:18,759] [INFO] DFAST_QC result json was written to OceanDNA-b17991/dqc_result.json
[2023-03-16 04:21:18,759] [INFO] DFAST_QC completed!
[2023-03-16 04:21:18,760] [INFO] Total running time: 0h0m35s