[2023-03-17 03:11:36,294] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,294] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference
[2023-03-17 03:11:37,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,489] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,489] [INFO] Running command: cat /var/lib/cwl/stgddb07df0-bfe2-45c3-93d7-bc27761e23c3/OceanDNA-b41307.fa | prodigal -d OceanDNA-b41307/cds.fna -a OceanDNA-b41307/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:12:21,309] [INFO] Task succeeded: Prodigal
[2023-03-17 03:12:21,309] [INFO] Task started: HMMsearch
[2023-03-17 03:12:21,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b41307/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference/reference_markers.hmm OceanDNA-b41307/protein.faa > /dev/null
[2023-03-17 03:12:21,605] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:12:21,606] [INFO] Found 6/6 markers.
[2023-03-17 03:12:21,644] [INFO] Query marker FASTA was written to OceanDNA-b41307/markers.fasta
[2023-03-17 03:12:21,644] [INFO] Task started: Blastn
[2023-03-17 03:12:21,645] [INFO] Running command: blastn -query OceanDNA-b41307/markers.fasta -db /var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference/reference_markers.fasta -out OceanDNA-b41307/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:26,447] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:26,447] [INFO] Selected 19 target genomes.
[2023-03-17 03:12:26,448] [INFO] Target genome list was writen to OceanDNA-b41307/target_genomes.txt
[2023-03-17 03:12:26,461] [INFO] Task started: fastANI
[2023-03-17 03:12:26,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgddb07df0-bfe2-45c3-93d7-bc27761e23c3/OceanDNA-b41307.fa --refList OceanDNA-b41307/target_genomes.txt --output OceanDNA-b41307/fastani_result.tsv --threads 1
[2023-03-17 03:12:56,370] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:56,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:56,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:56,383] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 03:12:56,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 03:12:56,383] [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
Pseudomonas cremoris	strain=WS 5106	GCA_014230465.1	2724178	2724178	type	True	99.3433	2081	2197	95	conclusive
Pseudomonas nabeulensis	strain=E10B	GCA_004682045.1	2293833	2293833	type	True	89.8825	1642	2197	95	below_threshold
Pseudomonas kairouanensis	strain=KC12	GCA_004682055.1	2293832	2293832	type	True	89.6469	1677	2197	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	88.661	1701	2197	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.659	1718	2197	95	below_threshold
Pseudomonas canadensis	strain=2-92	GCA_000503215.1	915099	915099	type	True	88.5861	1663	2197	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	88.4814	1621	2197	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_900111895.1	321846	321846	type	True	88.3874	1628	2197	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	88.3715	1638	2197	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.3309	1644	2197	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	87.9677	1574	2197	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	87.9224	1569	2197	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	87.7377	1568	2197	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	87.6574	1562	2197	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	86.5399	1631	2197	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	86.0678	1329	2197	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	86.0609	1351	2197	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.8022	1466	2197	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.0404	1290	2197	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:56,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41307/tc_result.tsv
[2023-03-17 03:12:56,383] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:56,383] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:56,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference/checkm_data
[2023-03-17 03:12:56,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:56,947] [INFO] Task started: CheckM
[2023-03-17 03:12:56,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41307/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41307/checkm_input OceanDNA-b41307/checkm_result
[2023-03-17 03:14:39,827] [INFO] Task succeeded: CheckM
[2023-03-17 03:14:39,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:14:39,831] [INFO] ===== Completeness check finished =====
[2023-03-17 03:14:39,832] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:14:39,832] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41307/markers.fasta)
[2023-03-17 03:14:39,833] [INFO] Task started: Blastn
[2023-03-17 03:14:39,833] [INFO] Running command: blastn -query OceanDNA-b41307/markers.fasta -db /var/lib/cwl/stg024a3a53-7d07-4a47-80dc-5e0db4d51072/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41307/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:14:41,372] [INFO] Task succeeded: Blastn
[2023-03-17 03:14:41,373] [INFO] Selected 17 target genomes.
[2023-03-17 03:14:41,373] [INFO] Target genome list was writen to OceanDNA-b41307/target_genomes_gtdb.txt
[2023-03-17 03:14:41,648] [INFO] Task started: fastANI
[2023-03-17 03:14:41,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgddb07df0-bfe2-45c3-93d7-bc27761e23c3/OceanDNA-b41307.fa --refList OceanDNA-b41307/target_genomes_gtdb.txt --output OceanDNA-b41307/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:15:09,437] [INFO] Task succeeded: fastANI
[2023-03-17 03:15:09,447] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:15:09,447] [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_014230465.1	s__Pseudomonas_E cremoris	99.3534	2081	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.87	96.78	0.87	0.83	4	conclusive
GCF_004682045.1	s__Pseudomonas_E nabeulensis	89.8825	1642	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.61	95.59	0.85	0.85	3	-
GCF_004682055.1	s__Pseudomonas_E kairouanensis	89.6483	1677	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	89.2893	1565	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612585.1	s__Pseudomonas_E sp000612585	88.8761	1630	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013386585.1	s__Pseudomonas_E sp013386585	88.7919	1653	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851685.1	s__Pseudomonas_E sp014851685	88.7692	1604	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385825.1	s__Pseudomonas_E reactans	88.6709	1688	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.45	96.30	0.89	0.87	7	-
GCF_000503215.1	s__Pseudomonas_E canadensis	88.5728	1664	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.83	97.74	0.94	0.91	12	-
GCF_003612935.1	s__Pseudomonas_E sp003013355	88.5009	1777	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.56	0.95	0.92	7	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	88.4835	1717	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_002979555.1	s__Pseudomonas_E sp002979555	88.4233	1485	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.44	99.31	0.96	0.95	11	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	88.4149	1670	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_900111895.1	s__Pseudomonas_E simiae	88.3948	1627	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.32	0.95	0.92	20	-
GCF_002563895.1	s__Pseudomonas_E lurida	88.3885	1636	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_900591205.1	s__Pseudomonas_E sp900591205	88.3828	1622	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	88.326	1609	2197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-17 03:15:09,448] [INFO] GTDB search result was written to OceanDNA-b41307/result_gtdb.tsv
[2023-03-17 03:15:09,448] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:15:09,450] [INFO] DFAST_QC result json was written to OceanDNA-b41307/dqc_result.json
[2023-03-17 03:15:09,450] [INFO] DFAST_QC completed!
[2023-03-17 03:15:09,450] [INFO] Total running time: 0h3m33s