[2023-03-18 01:54:19,452] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:19,452] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:19,452] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference
[2023-03-18 01:54:20,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:20,549] [INFO] Task started: Prodigal
[2023-03-18 01:54:20,549] [INFO] Running command: cat /var/lib/cwl/stg3a27128b-6a53-4061-9fe8-f0b80461b198/OceanDNA-b34471.fa | prodigal -d OceanDNA-b34471/cds.fna -a OceanDNA-b34471/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:44,452] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:44,453] [INFO] Task started: HMMsearch
[2023-03-18 01:54:44,453] [INFO] Running command: hmmsearch --tblout OceanDNA-b34471/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference/reference_markers.hmm OceanDNA-b34471/protein.faa > /dev/null
[2023-03-18 01:54:44,715] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:44,715] [INFO] Found 6/6 markers.
[2023-03-18 01:54:44,839] [INFO] Query marker FASTA was written to OceanDNA-b34471/markers.fasta
[2023-03-18 01:54:44,840] [INFO] Task started: Blastn
[2023-03-18 01:54:44,840] [INFO] Running command: blastn -query OceanDNA-b34471/markers.fasta -db /var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference/reference_markers.fasta -out OceanDNA-b34471/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:45,503] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:45,596] [INFO] Selected 11 target genomes.
[2023-03-18 01:54:45,597] [INFO] Target genome list was writen to OceanDNA-b34471/target_genomes.txt
[2023-03-18 01:54:45,604] [INFO] Task started: fastANI
[2023-03-18 01:54:45,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a27128b-6a53-4061-9fe8-f0b80461b198/OceanDNA-b34471.fa --refList OceanDNA-b34471/target_genomes.txt --output OceanDNA-b34471/fastani_result.tsv --threads 1
[2023-03-18 01:54:54,784] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:54,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:54,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:54,791] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 01:54:54,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:54:54,791] [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
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	97.687	1298	1431	95	conclusive
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	90.1429	1188	1431	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	88.3419	1070	1431	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	83.8404	903	1431	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	83.6241	915	1431	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	79.9745	395	1431	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:54:54,792] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34471/tc_result.tsv
[2023-03-18 01:54:54,793] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:54,793] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:54,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference/checkm_data
[2023-03-18 01:54:54,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:54,803] [INFO] Task started: CheckM
[2023-03-18 01:54:54,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34471/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34471/checkm_input OceanDNA-b34471/checkm_result
[2023-03-18 01:55:53,821] [INFO] Task succeeded: CheckM
[2023-03-18 01:55:53,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:55:53,860] [INFO] ===== Completeness check finished =====
[2023-03-18 01:55:53,860] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:55:53,860] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34471/markers.fasta)
[2023-03-18 01:55:53,862] [INFO] Task started: Blastn
[2023-03-18 01:55:53,862] [INFO] Running command: blastn -query OceanDNA-b34471/markers.fasta -db /var/lib/cwl/stg8ac0bdbe-6fb5-4473-9779-77e736d9e1aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34471/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:55:54,923] [INFO] Task succeeded: Blastn
[2023-03-18 01:55:54,933] [INFO] Selected 9 target genomes.
[2023-03-18 01:55:54,933] [INFO] Target genome list was writen to OceanDNA-b34471/target_genomes_gtdb.txt
[2023-03-18 01:55:54,938] [INFO] Task started: fastANI
[2023-03-18 01:55:54,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a27128b-6a53-4061-9fe8-f0b80461b198/OceanDNA-b34471.fa --refList OceanDNA-b34471/target_genomes_gtdb.txt --output OceanDNA-b34471/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:56:05,081] [INFO] Task succeeded: fastANI
[2023-03-18 01:56:05,087] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:56:05,087] [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_000172635.2	s__Alteromonas macleodii	97.687	1298	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	conclusive
GCF_000808575.1	s__Alteromonas marina	92.5588	1111	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_001953635.1	s__Alteromonas abrolhosensis	90.1335	1189	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_005117025.1	s__Alteromonas portus	88.3625	1068	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885075.1	s__Alteromonas sp001885075	86.2742	790	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	85.4285	1043	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000597705.1	s__Alteromonas sp000597705	84.6201	1044	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_003443615.1	s__Alteromonas sp003443615	84.6197	1021	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000020585.3	s__Alteromonas mediterranea	83.6341	914	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
--------------------------------------------------------------------------------
[2023-03-18 01:56:05,087] [INFO] GTDB search result was written to OceanDNA-b34471/result_gtdb.tsv
[2023-03-18 01:56:05,087] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:56:05,088] [INFO] DFAST_QC result json was written to OceanDNA-b34471/dqc_result.json
[2023-03-18 01:56:05,089] [INFO] DFAST_QC completed!
[2023-03-18 01:56:05,089] [INFO] Total running time: 0h1m46s