[2023-03-18 10:15:15,047] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,047] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,047] [INFO] DQC Reference Directory: /var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference
[2023-03-18 10:15:16,253] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,254] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,254] [INFO] Running command: cat /var/lib/cwl/stg60d7c1c9-35c0-4aa1-89dd-8263347b379b/OceanDNA-b18118.fa | prodigal -d OceanDNA-b18118/cds.fna -a OceanDNA-b18118/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:20,029] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:20,030] [INFO] Task started: HMMsearch
[2023-03-18 10:15:20,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b18118/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference/reference_markers.hmm OceanDNA-b18118/protein.faa > /dev/null
[2023-03-18 10:15:20,175] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:20,176] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60d7c1c9-35c0-4aa1-89dd-8263347b379b/OceanDNA-b18118.fa]
[2023-03-18 10:15:20,183] [INFO] Query marker FASTA was written to OceanDNA-b18118/markers.fasta
[2023-03-18 10:15:20,183] [INFO] Task started: Blastn
[2023-03-18 10:15:20,183] [INFO] Running command: blastn -query OceanDNA-b18118/markers.fasta -db /var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference/reference_markers.fasta -out OceanDNA-b18118/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:20,685] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:20,686] [INFO] Selected 19 target genomes.
[2023-03-18 10:15:20,686] [INFO] Target genome list was writen to OceanDNA-b18118/target_genomes.txt
[2023-03-18 10:15:20,719] [INFO] Task started: fastANI
[2023-03-18 10:15:20,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d7c1c9-35c0-4aa1-89dd-8263347b379b/OceanDNA-b18118.fa --refList OceanDNA-b18118/target_genomes.txt --output OceanDNA-b18118/fastani_result.tsv --threads 1
[2023-03-18 10:15:28,588] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:28,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:28,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:28,589] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:28,589] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:15:28,589] [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
--------------------------------------------------------------------------------
[2023-03-18 10:15:28,589] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18118/tc_result.tsv
[2023-03-18 10:15:28,590] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:28,590] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:28,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference/checkm_data
[2023-03-18 10:15:28,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:28,595] [INFO] Task started: CheckM
[2023-03-18 10:15:28,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18118/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18118/checkm_input OceanDNA-b18118/checkm_result
[2023-03-18 10:15:44,877] [INFO] Task succeeded: CheckM
[2023-03-18 10:15:44,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:15:44,878] [INFO] ===== Completeness check finished =====
[2023-03-18 10:15:44,879] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:15:44,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18118/markers.fasta)
[2023-03-18 10:15:44,880] [INFO] Task started: Blastn
[2023-03-18 10:15:44,880] [INFO] Running command: blastn -query OceanDNA-b18118/markers.fasta -db /var/lib/cwl/stg65ff8058-1b36-4c6f-8f94-15122fbe78da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18118/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:45,592] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:45,593] [INFO] Selected 13 target genomes.
[2023-03-18 10:15:45,593] [INFO] Target genome list was writen to OceanDNA-b18118/target_genomes_gtdb.txt
[2023-03-18 10:15:45,606] [INFO] Task started: fastANI
[2023-03-18 10:15:45,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d7c1c9-35c0-4aa1-89dd-8263347b379b/OceanDNA-b18118.fa --refList OceanDNA-b18118/target_genomes_gtdb.txt --output OceanDNA-b18118/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:15:47,722] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:47,730] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:15:47,730] [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_016777965.1	s__Marinisoma sp016777965	80.1537	70	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599655.1	s__Marinisoma sp902599655	80.0872	119	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_902538565.1	s__Marinisoma sp902538565	79.8711	158	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_902578385.1	s__Marinisoma sp002710515	79.7334	151	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_000402655.1	s__Marinisoma sp000402655	79.4087	160	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902576865.1	s__Marinisoma sp902576865	79.3918	124	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902526795.1	s__Marinisoma sp902526795	79.3475	134	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525615.1	s__Marinisoma sp902525615	79.1194	142	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624275.1	s__Marinisoma sp902624275	79.0891	136	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624575.1	s__Marinisoma sp902624575	79.0255	77	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402815.1	s__Marinisoma atlanticum	78.5066	96	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_002348725.1	s__Marinisoma sp002348725	77.1277	60	248	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.66	99.62	0.84	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-18 10:15:47,730] [INFO] GTDB search result was written to OceanDNA-b18118/result_gtdb.tsv
[2023-03-18 10:15:47,731] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:15:47,731] [INFO] DFAST_QC result json was written to OceanDNA-b18118/dqc_result.json
[2023-03-18 10:15:47,732] [INFO] DFAST_QC completed!
[2023-03-18 10:15:47,732] [INFO] Total running time: 0h0m33s