[2023-03-15 04:05:08,790] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:05:08,792] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:05:08,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference
[2023-03-15 04:05:09,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:05:09,872] [INFO] Task started: Prodigal
[2023-03-15 04:05:09,872] [INFO] Running command: cat /var/lib/cwl/stgc891a98a-5e10-4e7b-8f73-37735d78ae5d/OceanDNA-b9654.fa | prodigal -d OceanDNA-b9654/cds.fna -a OceanDNA-b9654/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:05:22,103] [INFO] Task succeeded: Prodigal
[2023-03-15 04:05:22,103] [INFO] Task started: HMMsearch
[2023-03-15 04:05:22,103] [INFO] Running command: hmmsearch --tblout OceanDNA-b9654/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference/reference_markers.hmm OceanDNA-b9654/protein.faa > /dev/null
[2023-03-15 04:05:22,261] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:05:22,261] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc891a98a-5e10-4e7b-8f73-37735d78ae5d/OceanDNA-b9654.fa]
[2023-03-15 04:05:22,310] [INFO] Query marker FASTA was written to OceanDNA-b9654/markers.fasta
[2023-03-15 04:05:22,312] [INFO] Task started: Blastn
[2023-03-15 04:05:22,312] [INFO] Running command: blastn -query OceanDNA-b9654/markers.fasta -db /var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference/reference_markers.fasta -out OceanDNA-b9654/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:05:22,768] [INFO] Task succeeded: Blastn
[2023-03-15 04:05:22,775] [INFO] Selected 13 target genomes.
[2023-03-15 04:05:22,776] [INFO] Target genome list was writen to OceanDNA-b9654/target_genomes.txt
[2023-03-15 04:05:22,782] [INFO] Task started: fastANI
[2023-03-15 04:05:22,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgc891a98a-5e10-4e7b-8f73-37735d78ae5d/OceanDNA-b9654.fa --refList OceanDNA-b9654/target_genomes.txt --output OceanDNA-b9654/fastani_result.tsv --threads 1
[2023-03-15 04:05:30,656] [INFO] Task succeeded: fastANI
[2023-03-15 04:05:30,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:05:30,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:05:30,670] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:05:30,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:05:30,670] [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
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	79.1636	293	555	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	79.0861	281	555	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	78.5889	231	555	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	78.3561	241	555	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	78.3112	239	555	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	78.2829	242	555	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	78.1866	252	555	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	78.1277	237	555	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:05:30,674] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9654/tc_result.tsv
[2023-03-15 04:05:30,678] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:05:30,678] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:05:30,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference/checkm_data
[2023-03-15 04:05:30,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:05:30,851] [INFO] Task started: CheckM
[2023-03-15 04:05:30,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9654/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9654/checkm_input OceanDNA-b9654/checkm_result
[2023-03-15 04:06:06,235] [INFO] Task succeeded: CheckM
[2023-03-15 04:06:06,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:06:06,401] [INFO] ===== Completeness check finished =====
[2023-03-15 04:06:06,402] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:06:06,402] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9654/markers.fasta)
[2023-03-15 04:06:06,403] [INFO] Task started: Blastn
[2023-03-15 04:06:06,403] [INFO] Running command: blastn -query OceanDNA-b9654/markers.fasta -db /var/lib/cwl/stgdbfbf36d-9c4b-4432-9044-a7296b2c2c57/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9654/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:06:07,064] [INFO] Task succeeded: Blastn
[2023-03-15 04:06:07,071] [INFO] Selected 13 target genomes.
[2023-03-15 04:06:07,071] [INFO] Target genome list was writen to OceanDNA-b9654/target_genomes_gtdb.txt
[2023-03-15 04:06:07,084] [INFO] Task started: fastANI
[2023-03-15 04:06:07,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgc891a98a-5e10-4e7b-8f73-37735d78ae5d/OceanDNA-b9654.fa --refList OceanDNA-b9654/target_genomes_gtdb.txt --output OceanDNA-b9654/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:06:15,388] [INFO] Task succeeded: fastANI
[2023-03-15 04:06:15,393] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:06:15,393] [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_005771495.1	s__Maribacter sp005771495	79.8869	305	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	79.1636	293	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	79.0861	281	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	78.5889	231	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	78.4733	227	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	78.2878	241	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112245.1	s__Maribacter stanieri	78.1866	252	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_004364165.1	s__Maribacter spongiicola	78.1277	237	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:06:15,396] [INFO] GTDB search result was written to OceanDNA-b9654/result_gtdb.tsv
[2023-03-15 04:06:15,401] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:06:15,405] [INFO] DFAST_QC result json was written to OceanDNA-b9654/dqc_result.json
[2023-03-15 04:06:15,406] [INFO] DFAST_QC completed!
[2023-03-15 04:06:15,406] [INFO] Total running time: 0h1m7s