[2023-03-17 14:06:37,932] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:06:37,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:06:37,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference
[2023-03-17 14:06:39,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:06:39,411] [INFO] Task started: Prodigal
[2023-03-17 14:06:39,411] [INFO] Running command: cat /var/lib/cwl/stg072216f1-4d3d-4b84-98bc-e9979cc87136/OceanDNA-b23008.fa | prodigal -d OceanDNA-b23008/cds.fna -a OceanDNA-b23008/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:06:55,173] [INFO] Task succeeded: Prodigal
[2023-03-17 14:06:55,173] [INFO] Task started: HMMsearch
[2023-03-17 14:06:55,173] [INFO] Running command: hmmsearch --tblout OceanDNA-b23008/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference/reference_markers.hmm OceanDNA-b23008/protein.faa > /dev/null
[2023-03-17 14:06:55,363] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:06:55,364] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg072216f1-4d3d-4b84-98bc-e9979cc87136/OceanDNA-b23008.fa]
[2023-03-17 14:06:55,391] [INFO] Query marker FASTA was written to OceanDNA-b23008/markers.fasta
[2023-03-17 14:06:55,391] [INFO] Task started: Blastn
[2023-03-17 14:06:55,391] [INFO] Running command: blastn -query OceanDNA-b23008/markers.fasta -db /var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference/reference_markers.fasta -out OceanDNA-b23008/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:06:55,984] [INFO] Task succeeded: Blastn
[2023-03-17 14:06:55,985] [INFO] Selected 25 target genomes.
[2023-03-17 14:06:55,985] [INFO] Target genome list was writen to OceanDNA-b23008/target_genomes.txt
[2023-03-17 14:06:56,000] [INFO] Task started: fastANI
[2023-03-17 14:06:56,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg072216f1-4d3d-4b84-98bc-e9979cc87136/OceanDNA-b23008.fa --refList OceanDNA-b23008/target_genomes.txt --output OceanDNA-b23008/fastani_result.tsv --threads 1
[2023-03-17 14:07:12,895] [INFO] Task succeeded: fastANI
[2023-03-17 14:07:12,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:07:12,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:07:12,904] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:07:12,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:07:12,904] [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
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.9638	72	844	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.9626	68	844	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.9621	73	844	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.9614	68	844	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.916	77	844	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	74.9021	50	844	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8587	100	844	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	74.8491	50	844	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.7931	102	844	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	74.7276	55	844	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.7024	62	844	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	74.6517	60	844	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	74.5816	56	844	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:07:12,904] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23008/tc_result.tsv
[2023-03-17 14:07:12,904] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:07:12,904] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:07:12,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference/checkm_data
[2023-03-17 14:07:12,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:07:12,911] [INFO] Task started: CheckM
[2023-03-17 14:07:12,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23008/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23008/checkm_input OceanDNA-b23008/checkm_result
[2023-03-17 14:07:53,745] [INFO] Task succeeded: CheckM
[2023-03-17 14:07:53,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:07:53,748] [INFO] ===== Completeness check finished =====
[2023-03-17 14:07:53,748] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:07:53,748] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23008/markers.fasta)
[2023-03-17 14:07:53,749] [INFO] Task started: Blastn
[2023-03-17 14:07:53,749] [INFO] Running command: blastn -query OceanDNA-b23008/markers.fasta -db /var/lib/cwl/stgcb1f513b-bc43-4856-a734-cbe93fb32d04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23008/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:07:54,613] [INFO] Task succeeded: Blastn
[2023-03-17 14:07:54,614] [INFO] Selected 19 target genomes.
[2023-03-17 14:07:54,614] [INFO] Target genome list was writen to OceanDNA-b23008/target_genomes_gtdb.txt
[2023-03-17 14:07:54,755] [INFO] Task started: fastANI
[2023-03-17 14:07:54,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg072216f1-4d3d-4b84-98bc-e9979cc87136/OceanDNA-b23008.fa --refList OceanDNA-b23008/target_genomes_gtdb.txt --output OceanDNA-b23008/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:08:09,024] [INFO] Task succeeded: fastANI
[2023-03-17 14:08:09,034] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 14:08:09,034] [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_011053145.1	s__DRLC01 sp011053145	77.7848	238	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DRLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	77.459	237	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140785.1	s__JABFRZ01 sp013140785	77.3813	185	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	77.1392	326	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360535.1	s__F1-120-MAGs118 sp013360535	76.9993	149	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.9363	161	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	76.8763	150	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_016712565.1	s__JADJQU01 sp016712565	76.8593	138	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	76.8333	200	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	76.6613	179	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125265.1	s__RI-242 sp016125265	76.5727	134	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RI-242	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751255.1	s__Pla86 sp007751255	76.5122	221	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016709875.1	s__JADJLZ01 sp016709875	76.5029	210	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	76.1017	154	844	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709145.1	s__JADJEK01 sp016709145	75.391	97	844	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879945.1	s__JAEUJQ01 sp014879945	74.8739	92	844	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642635.1	s__Aureimonas_A endophytica	74.7198	57	844	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:08:09,034] [INFO] GTDB search result was written to OceanDNA-b23008/result_gtdb.tsv
[2023-03-17 14:08:09,034] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:08:09,036] [INFO] DFAST_QC result json was written to OceanDNA-b23008/dqc_result.json
[2023-03-17 14:08:09,036] [INFO] DFAST_QC completed!
[2023-03-17 14:08:09,036] [INFO] Total running time: 0h1m31s