[2023-03-16 17:42:49,386] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:42:49,386] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:42:49,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference
[2023-03-16 17:42:51,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:42:51,191] [INFO] Task started: Prodigal
[2023-03-16 17:42:51,191] [INFO] Running command: cat /var/lib/cwl/stg4a9bb2f1-b636-45e1-8d3a-51376b95f3d0/OceanDNA-b32271.fa | prodigal -d OceanDNA-b32271/cds.fna -a OceanDNA-b32271/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:43:14,935] [INFO] Task succeeded: Prodigal
[2023-03-16 17:43:14,936] [INFO] Task started: HMMsearch
[2023-03-16 17:43:14,936] [INFO] Running command: hmmsearch --tblout OceanDNA-b32271/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference/reference_markers.hmm OceanDNA-b32271/protein.faa > /dev/null
[2023-03-16 17:43:15,143] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:43:15,144] [INFO] Found 6/6 markers.
[2023-03-16 17:43:15,165] [INFO] Query marker FASTA was written to OceanDNA-b32271/markers.fasta
[2023-03-16 17:43:15,166] [INFO] Task started: Blastn
[2023-03-16 17:43:15,166] [INFO] Running command: blastn -query OceanDNA-b32271/markers.fasta -db /var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference/reference_markers.fasta -out OceanDNA-b32271/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:43:15,911] [INFO] Task succeeded: Blastn
[2023-03-16 17:43:15,912] [INFO] Selected 17 target genomes.
[2023-03-16 17:43:15,912] [INFO] Target genome list was writen to OceanDNA-b32271/target_genomes.txt
[2023-03-16 17:43:15,922] [INFO] Task started: fastANI
[2023-03-16 17:43:15,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a9bb2f1-b636-45e1-8d3a-51376b95f3d0/OceanDNA-b32271.fa --refList OceanDNA-b32271/target_genomes.txt --output OceanDNA-b32271/fastani_result.tsv --threads 1
[2023-03-16 17:43:34,108] [INFO] Task succeeded: fastANI
[2023-03-16 17:43:34,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:43:34,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:43:34,119] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:43:34,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:43:34,119] [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
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	84.2848	793	1089	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.6085	365	1089	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.2206	394	1089	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.1367	356	1089	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.0804	328	1089	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.9511	164	1089	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	76.8537	184	1089	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.8251	150	1089	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	76.7991	152	1089	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	76.73	124	1089	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	76.5248	105	1089	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.5005	101	1089	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.4867	127	1089	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	76.3268	112	1089	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.2787	128	1089	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	76.2206	99	1089	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	76.165	103	1089	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:43:34,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32271/tc_result.tsv
[2023-03-16 17:43:34,119] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:43:34,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:43:34,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference/checkm_data
[2023-03-16 17:43:34,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:43:34,126] [INFO] Task started: CheckM
[2023-03-16 17:43:34,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32271/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32271/checkm_input OceanDNA-b32271/checkm_result
[2023-03-16 17:44:42,687] [INFO] Task succeeded: CheckM
[2023-03-16 17:44:42,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:44:42,690] [INFO] ===== Completeness check finished =====
[2023-03-16 17:44:42,690] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:44:42,690] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32271/markers.fasta)
[2023-03-16 17:44:42,692] [INFO] Task started: Blastn
[2023-03-16 17:44:42,692] [INFO] Running command: blastn -query OceanDNA-b32271/markers.fasta -db /var/lib/cwl/stg1237395f-400f-4cb7-beb2-b02d1fd5f029/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32271/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:44:44,046] [INFO] Task succeeded: Blastn
[2023-03-16 17:44:44,047] [INFO] Selected 9 target genomes.
[2023-03-16 17:44:44,047] [INFO] Target genome list was writen to OceanDNA-b32271/target_genomes_gtdb.txt
[2023-03-16 17:44:44,184] [INFO] Task started: fastANI
[2023-03-16 17:44:44,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a9bb2f1-b636-45e1-8d3a-51376b95f3d0/OceanDNA-b32271.fa --refList OceanDNA-b32271/target_genomes_gtdb.txt --output OceanDNA-b32271/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:44:50,459] [INFO] Task succeeded: fastANI
[2023-03-16 17:44:50,466] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:44:50,466] [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_905479715.1	s__Parasphingorhabdus sp905479715	85.1965	671	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	84.2776	794	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	84.2458	791	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	83.7001	802	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	83.1021	460	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	83.0423	728	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	82.7548	580	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	82.6454	731	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	82.3453	713	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:44:50,466] [INFO] GTDB search result was written to OceanDNA-b32271/result_gtdb.tsv
[2023-03-16 17:44:50,466] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:44:50,468] [INFO] DFAST_QC result json was written to OceanDNA-b32271/dqc_result.json
[2023-03-16 17:44:50,468] [INFO] DFAST_QC completed!
[2023-03-16 17:44:50,468] [INFO] Total running time: 0h2m1s